Container Line Supply Chain (CLSC), which transports cargo in containers and accounts for approximately 95 percent of world trade, is a dominant way for world cargo transportation due to its high efficiency. However, the operation of a typical CLSC, which may involve as many as 25 different organizations spreading all over the world, is very complex, and at the same time, it is estimated that only 2 percent of imported containers are physically inspected in most countries. The complexity together with insufficient prevention measures makes CLSC vulnerable to many threats, such as cargo theft, smuggling, stowaway, terrorist activity, piracy, etc. Furthermore, as disruptions caused by a security incident in a certain point along a CLSC may also cause disruptions to other organizations involved in the same CLSC, the consequences of security incidents to a CLSC may be severe. Therefore, security analysis becomes essential to ensure smooth operation of CLSC, and more generally, to ensure smooth development of world economy. The literature review shows that research on CLSC security only began recently, especially after the terrorist attack on September 11th, 2001, and most of the research either focuses on developing policies, standards, regulations, etc. to improve CLSC security from a general view or focuses on discussing specific security issues in CLSC in a descriptive and subjective way. There is a lack of research on analytical security analysis to provide specific, feasible and practical assistance for people in governments, organizations and industries to improve CLSC security. Facing the situation mentioned above, this thesis intends to develop a set of analytical models for security analysis in CLSC to provide practical assistance to people in maintaining and improving CLSC security. In addition, through the development of the models, the thesis also intends to provide some methodologies for general risk/security analysis problems under complex and uncertain environment, and for some general complex decision problems under uncertainty. Specifically, the research conducted in the thesis is mainly aimed to answer the following two questions: how to assess security level of a CLSC in an analytical and rational way, and according to the security assessment result, how to develop balanced countermeasures to improve security level of a CLSC under the constraints of limited resources. For security assessment, factors influencing CLSC security as a whole are identified first and then organized into a general hierarchical model according to the relations among the factors. The general model is then refined for security assessment of a port storage area along a CLSC against cargo theft. Further, according to the characteristics of CLSC security analysis, the belief Rule base Inference Methodology using the Evidential Reasoning approach (RIMER) is selected as the tool to assess CLSC security due to its capabilities in accommodating and handling different forms of information with different kinds of uncertainty involved in both the measurement of factors identified and the measurement of relations among the factors. To build a basis of the application of RIMER, a new process is introduced to generate belief degrees in Belief Rule Bases (BRBs), with the aim of reducing bias and inconsistency in the process of the generation. Based on the results of CLSC security assessment, a novel resource allocation model for security improvement is also proposed within the framework of RIMER to optimally improve CLSC security under the constraints of available resources. In addition, it is reflected from the security assessment process that RIMER has its limitations in dealing with different information aggregation patterns identified in the proposed security assessment model, and in dealing with different kinds of incompleteness in CLSC security assessment. Correspondently, under the framework of RIMER, novel methods are proposed to accommodate and handle different information aggregation patterns, as well as different kinds of incompleteness. To validate the models proposed in the thesis, several case studies are conducted using data collected from different ports in both the UK and China. From a methodological point of view, the ideas, process and models proposed in the thesis regarding BRB generation, optimal resource allocation based on security assessment results, information aggregation pattern identification and handling, incomplete information handling can be applied not only for CLSC security analysis, but also for dealing with other risk and security analysis problems and more generally, some complex decision problems. From a practical point of view, the models proposed in the thesis can help people in governments, organizations, and industries related to CLSC develop best practices to ensure secure operation, assess security levels of organizations involved in a CLSC and security level of the whole CLSC, and allocate limited resources to improve security of organizations in CLSC. The potential beneficiaries of the research may include: governmental organizations, international/regional organizations, industrial organizations, classification societies, consulting companies, companies involved in a CLSC, companies with cargo to be shipped, individual researchers in relevant areas etc.