Thermal management systems are critical to the maintenance of lithium-ion battery performance in new energy vehicles. While phase change materials are frequently employed in battery thermal management systems, it’s important to address the concerns related to their leakage and flammability, as they can pose hazards to the safety performance of batteries. This paper proposes a novel flame retardant composite phase change material (CPCM) consisting of paraffin, high-density polyethylene, expanded graphite, ammonium polyphosphate, red phosphorus, and zinc oxide. The performance of CPCMs containing different ratios of flame retardants is investigated, and their effects when applied to battery thermal management systems are compared. The results demonstrate that the leakage rate of the flame retardant CPCMs is maintained within 1%, indicating excellent flame retardant performance and thermal management efficiency. The combination of ammonium polyphosphate and red phosphorus in the flame retardant exhibits effective synergistic effects, while zinc oxide may help phosphate compounds create their bridging bonds, which would then make it possible to construct a char layer that would separate heat and oxygen. Under a 2C discharge rate, the maximum temperature of the battery pack remains below 50 °C, and the temperature difference can be controlled within 5 °C. Even under a 3C discharge rate, the maximum temperature and temperature difference are reduced by 30.31% and 29.53%, respectively.