This study explores the performance enhancement of an innovative multi-layer solar cell structure using the SCAPS-1D (Solar Cell Capacitance Simulator in One Dimension) software. We aim to improve the efficiency of a solar cell structure comprising ZnO/ZnSe/CZTSe/CuInSe2/CZTSSe/Mo by incorporating CZTSe as the upper absorber layer, CuInSe2 as the main absorber layer, and CZTSSe as a back surface field (BSF) layer. Initially, we compare the performance of three different configurations by analyzing their J-V characteristics. For the best performing structure, we further examine the external quantum efficiency (EQE) spectrum. We then evaluate various window (ZnO, ZnMgO, SnO2, Zn2SnO4) and buffer (ZnSe, ZrS2, SnS2, In2S3) materials, identifying ZnO and ZrS2 as the most effective for achieving high current density and efficiency. Through detailed simulations, we determine the optimal thicknesses for CZTSSe (0.2 µm), CZTSe (0.4 µm), and CuInSe2 (3.2 µm). Additionally, by optimizing the acceptor density to 1020 cm−3, we significantly enhance the performance of both CZTSe and CZTSSe layers. Temperature management is shown to be crucial, with the highest efficiency observed at 300 K. As a result of these optimizations, the solar cell structure achieves a remarkable efficiency of 35.38%. Furthermore, we compare our results with existing literature to highlight the advancements made in this study. These findings underscore the importance of material selection and structural optimization in developing high-efficiency solar cells and provide a framework for future advancements in photovoltaic technology.