To address the problems of high preheating energy consumption and endurance anxiety in fuel cell vehicles (FCVs) in low-temperature environments, this study proposes a novel, three heat source heat pump integrated thermal management system (AFMHP ITMS) based on the collaborative adjustment of the refrigerant flow distribution ratio. When the working temperatures of the different heat sources change, the proposed AFMHP ITMS can dynamically adjust the distribution ratio of the refrigerant flow in each heat source circuit to achieve the most efficient recovery of air, fuel cell, and motor heat and thereby achieve the lowest energy consumption. Specifically, this study proposes a highly integrated thermal management system, establishes an integrated thermal management system model, and validates the model. Subsequently, a hierarchical collaborative control strategy is proposed. The upper layer collaboratively adjusts the preheating power of the cabin and battery based on nonlinear model predictive control (MPC), whereas the lower layer adjusts the distribution of refrigerant flow in each heat source circuit based on a genetic algorithm. Finally, the effectiveness of the proposed AFMHP ITMS was verified via simulation and a hardware-in-the-loop (HIL) test. The results show that, compared with non- collaborative control, the hierarchical collaborative control strategy results in energy savings of 10.7-11.3%. Moreover, the differences between the simulation and HIL results are small, which proves the real-time performance of the proposed strategy. Compared with positive temperature coefficient (PTC) preheating, the proposed AFMHP ITMS results in energy savings of 17.8-34.3%. This study provides a new solution for alleviating endurance anxiety in fuel cell vehicles operating in low-temperature environments.