Computational modeling has become essential for understanding and optimizing the nanoscale processes that are critical to supercapacitor performance. This review highlights recent molecular simulations of advanced nanomaterials for supercapacitors, emphasizing nanoporous carbonsNanoporous carbon, conductive metal-organic frameworks (cMOFsConductive MOFs (cMOFs)), and two-dimensional layered materials such as MXenesMXenes and transition metal dichalcogenidesTransition Metal Dichalcogenides (TMDs). Key findings include the discovery that anomalous capacitanceAnomalous capacitance enhancementCapacitance in nanoporous carbonsNanoporous carbon arises from optimal ion confinement and structural disorder, as demonstrated through constant potential molecular dynamics. For cMOFsConductive MOFs (cMOFs), high-throughput density functional theoryDensity Functional Theory (DFT) screening has identified frameworks with high electronic conductivityElectronic conductivity, while molecular simulations have clarified the relationship between pore structure, ionic mobility, and interfacial capacitanceCapacitance, with values in good agreement with experimental observations. Sophisticated constant potential models for heterogeneous electrodes, such as constant chemical potential method, revealed unique charge-storage mechanisms in layered 2D materials, including dominant co-ion desorptionCo-ion desorption in metallic 1T-MoS \(_{2}\) 1T-MoS2. The review also identifies challenges, including limitations in accurately modeling redox reactionsRedox reactions, scalability of quantum-mechanical methods, and the need for diverse machine-learning training datasets. Overcoming these challenges requires developing multiscale modeling and continued synergy between simulation and experiment, paving the way for the rational design of next-generation supercapacitor materials.