Efficient thermal regulation is critical for the safe and reliable operation of lithium-ion batteries in electric vehicles and energy storage systems; however, conventional battery thermal management systems (BTMSs) often fail to ensure rapid response and stable temperature control under dynamic operating conditions. This study aims to develop a high-performance hybrid BTMS that couples thermoelectric coolers (TECs) with PCMs and to investigate its transient thermal response, synergistic cooling mechanism, and optimization potential under realistic, time-varying battery heat generation. A three-dimensional multi-physics transient numerical model was established, incorporating thermoelectric conversion, PCM phase change behavior, fluid-solid coupled heat transfer, and dynamic battery heat generation characteristics under WLTP conditions. Comparative analyses were conducted among three systems: (1) TEC-PCM hybrid BTMS, (2) liquid cooling + PCM BTMS, and (3) PCM-only BTMS. The effects of PCM type and TEC operating current were also evaluated to determine optimal system configurations. The TEC-PCM hybrid BTMS exhibited the best thermal control, maintaining the battery temperature below 312.23 K with a maximum temperature difference of only 3.67 K, extending PCM operation up to 5400 s. A strong synergistic effect between TEC and PCM was observed: TECs provided rapid active cooling under high loads and facilitated PCM latent heat recovery during low loads. Optimization revealed that combining PCM 3 (high latent heat) with a TEC current of 0.9 A achieved the most efficient performance, with a maximum temperature of 311.31 K, a maximum temperature difference of 3.66 K, and a PCM liquid fraction of 0.985. The proposed TEC-PCM hybrid BTMS effectively addresses the limitations of conventional systems by combining fast thermoelectric response and high-capacity latent heat buffering. Its robust transient regulation and optimization potential make it a promising solution for next-generation electric vehicle battery cooling and energy storage applications.