A control method and system of a fuel cell electric vehicle stack. The control method comprises obtaining insulation resistance of the stack, comprising at least two sub-stacks connected in parallel; and disconnecting a sub-stack with insulation failure from a DC bus and then causing the stack to enter a failure mode when it is determined that the insulation resistance of the stack is smaller than a first preset threshold. The stack is determined to have an insulation failure when it is determined that the insulation resistance of the stack is smaller than the first preset threshold. The sub-stack with the insulation failure is located and disconnected the sub-stack with insulation failure from a DC bus, and the stack is then caused to run in a failure mode to perform failure protection, avoid deterioration of the insulation failure and burnout of the stack and improve the safety performance of the stack.