New satellite missions have provided High Resolution (HR) Satellite Image Time Series (SITS), offering detailed spatial, spectral, and temporal information for effective monitoring of diverse Earth features including weather, landforms, oceans, vegetation, and agricultural practices. SITS can be used for an accurate understanding of the Land Cover (LC) behavior and providing the possibility of precise mapping of LCs. Moreover, HR SITS presents an unprecedented possibility for the creation and modification of HR Land Cover Change (LCC) and Land Cover Transition (LCT) maps. For the long-term scale, spanning multiple years, it becomes feasible to analyze LCC and the LCTs occurring between consecutive years. Existing methods in literature often analyze bi-temporal images and miss the valuable multi-temporal/multi-annual information of SITS that is crucial for an accurate SITS analysis. As a result, HR SITS necessitates a paradigm shift in processing and methodology development, introducing new challenges in data handling. Yet, the creation of techniques that can effectively manage the high spatial correlation and complementary temporal resolutions of pixels remains paramount. Moreover, the temporal availability of HR data across historical and current archives varies significantly, creating the need for an effective preprocessing to account for factors like atmospheric and radiometric conditions that can affect image reflectance and their applicability in SITS analysis. Flexible and automatic SITS analysis methods can be developed by paying special attention to handling big amounts of data and modeling the correlation and characterization of SITS in space and time. Novel methods should deal with data preparation and pre-processing at large-scale from end-to-end by introducing a set of steps that guarantee reliable SITS analysis while upholding the computational efficiency for a feasible SITS analysis. In this context, the recent strides in deep learning-based frameworks have demonstrated their potential across various image processing tasks, and thus the high relevance for addressing SITS analysis. Deep learning-based methods can be supervised or unsupervised considering their learning process. Supervised deep learning methods rely on labeled training data, which can be impractical for large-scale multi-temporal datasets, due to the challenges of manual labeling. In contrast, unsupervised deep learning methods are favored as they can automatically discover temporal patterns and changes without the need for labeled samples, thereby reducing the computational load, making them more suitable for handling extensive SITS. In this scenario, the objectives of this thesis are mainly three. Firstly, it seeks to establish a robust and reliable framework for the precise mapping of LCs by designing novel techniques for time series analysis. Secondly, it aims to utilize the capacities of unsupervised deep learning methods, such as pretrained Convolutional Neural Networks (CNNs), to construct a comprehensive methodology for Change Detection (CD), thereby mitigating complexity and reducing computational requirements in comparison with supervised methods. This involves the efficient extraction of spatial, spectral, and temporal features from complex multi-temporal, multi-spectral SITS. Lastly, the thesis endeavors to develop novel methods for analyzing LCCs occurring over extended time periods, spanning multiple years. This multifaceted approach encompasses the detection of changes, timing identification, and classification of the specific types of LCTs. The efficacy of the innovative methodologies and associated techniques is showcased through a series of experiments conducted on HR SITS datasets, including those from Sentinel-2 and Landsat. These experiments reveal significant enhancements when compared to existing methods that represent the current state-of-the-art.