The electric vehicle thermal management system (EVTMS) plays a crucial role in ensuring battery efficiency, driving range, and passenger comfort. However, EVTMSs still face unresolved challenges, such as accurate modeling, compensating for temperature variations, and achieving efficient control strategies. Addressing these issues is crucial for enhancing the performance, reliability, and energy efficiency of electric vehicles. Therefore, this study presents a cooling EVTMS model, considering both the battery pack temperature and the cabin comfort, and utilizes the prediction of neural network as a feedforward in a fuzzy PI controller to compensate for the model temperature variations. The simulation results reveal that, compared with PI controller and MPC, the neural network fuzzy PI (NN-Fuzzy PI) controller can well predict and compensate for the system’s nonlinear characteristics as well as the time-delay caused by heat transfer, achieving superior control performance and reducing energy consumption. The battery pack temperature and PMV fluctuations are effectively constrained within [−0.5, 0.5] and [−0.1, 0.1], reducing up to 150% and 164%, and the energy consumption of the pump and compressor are reduced by up to 0.23 and 100.1 KJ, with ranges of 18% and 2.68%. Meanwhile, the neural network feedforward also works effectively in different controllers. The findings of this research can provide valuable insights for TMS engineers to select advanced control strategies.