Batteries with high energy density are packed into compact groups to solve the range anxiety of new-energy vehicles, which brings greater workload and insecurity, risking thermal runaway in harsh conditions. To improve the battery thermal performance under high ambient temperature and discharge rate, a battery thermal management system (BTMS) based on honeycomb-structured liquid cooling and phase change materials (PCM) is innovatively proposed. In this paper, the thermal characteristics of INR18650/25P battery are studied theoretically and experimentally. Moreover, the influence of structure, material and operating parameters are studied based on verifying the simplified BTMS model. The results show that the counterflow, honeycomb structure of six cooling tubes and fins, 12% expanded graphite mass fraction and 25 mm battery spacing give a better battery thermal performance with high group efficiency. The maximum temperature and temperature difference in the battery in the optimal BTMS are 45.71 °C and 4.4 °C at the 40 °C environment/coolant, as against 30.4 °C and 4.97 °C at the 23.6 °C environment/coolant, respectively. Precooling the coolant can further reduce the maximum battery temperature in high temperature environments, and the precooling temperature difference within 5 °C could meet the uniformity requirements. Furthermore, this study can provide guidance for the design and optimization of BTMS under harsh conditions.