Aiming at the risks of overcharge, overdischarge and thermal runaway induced by the communication interruption between VCU and BMS of fuel cell commercial vehicles, this paper conducts hazard analysis and risk assessment based on the ISO 26262 standard, and proposes a hierarchical vehicle control strategy. The strategy integrates critical signal timeout detection, two-level graded response of limp-home mode and immediate power-off, and scenario-based processing methods. Meanwhile, it adopts an SOC estimation model combining bus voltage integration and accessory power estimation, and designs a fault tolerance and recovery confirmation mechanism for thermal management system. Real vehicle verification results show that the fault detection time is 300ms, the SOC estimation error is within 5%, the limp-home mileage under various working conditions ranges from 7.6km to 19.5km, and the stack shutdown time is 2.7s to 3.2s. The proposed strategy ensures vehicle functional safety while retaining the limp-home capability, which provides a valuable engineering reference for communication fault protection of fuel cell commercial vehicles.