Potential parameters that can handle multi-component oxide glass systems especially boron oxide are very limited in literature. One of the main goals of my dissertation is to develop empirical potentials to simulate multi-component oxide glass systems with boron oxide. Two approaches, both by introducing the composition dependent parameter feature, were taken and both led to successful potentials for boron containing glass systems after extensive testing and fitting. Both potential sets can produce reasonable glass structures of the multi-component oxide glass systems, with structure and properties in good agreement with experimental data. Furthermore, we have tested the simulation settings such as system size and cooling rate effects on the results of structures and properties of MD simulated borosilicate glasses. It was found that increase four-coordinated boron with decreasing cooling rate and system size above 1000 atoms is necessary to produce converged structure. Another application of the potentials is to simulate a six-component nuclear waste glass, international simple glass (ISG), which was for first time simulated using the newly developed parameters. Structural features obtained from simulations agree well with the experimental results. In addition, two series of sodium borosilicate and boroaluminosilicate glasses were simulated with the two sets of potentials to compare and evaluate their applicability and deficiency. Various analyses on the structures and properties such as pair distribution function, total correlation function, coordination number analysis, Qn distribution function, ring size distribution function, vibrational density of states and mechanical properties were performed. This work highlights the challenge of MD simulations of boron containing glasses and the capability of the new potential parameters that enable simulations of wide range of mixed former glasses to investigate new structure features and design of new glass compositions for various applications.