The performance of lithium-ion batteries tends to deteriorate over time due to various chemical changes. This deterioration in performance is governed by a small layer called the solid electrolyte interphase (SEI). The SEI is a nanometer thin heterogeneous layer that forms at the anode/electrolyte interface due to the reduction of the electrolyte by electrons from the anode. The initial formation of the SEI protects the electrolyte from further reduction, hence, stabilizing the battery. However, the SEI layer experiences various chemical changes and grows over time consuming active electrons and electrolyte species leading to capacity loss and eventually the death of the battery. In this thesis, we shed light on the formation and growth of the SEI layer using molecular modeling techniques. The main challenge for molecular modeling is that the changes leading to the SEI growth and capacity loss take place at different timescales. Hence, we have used various molecular modeling techniques to tackle this problem. Due to the high computational cost of the first principles computations (e.g., DFT), we used in two complementary contexts. The first approach is to benchmark low-cost electron structure methods to identify the most appropriate one to be used to model SEI chemistry. The second approach is to investigate major decomposition reaction pathways using DFT. Then, we used kinetic Monte Carlo (kMC) simulation method to explore the time evolution of the capacity loss and extend the length scale of the SEI model. Our results predicted a multi-layered SEI structure and behaviors of the capacity loss over time in agreement with previous experimental and theoretical studies.