A control method and system of a fuel cell electric vehicle stack. The control method comprises steps of: obtaining insulation resistance of the stack, which comprises at least two sub-stacks electrically 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 a first preset threshold. The sub-stack that has 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 on the stack, avoid deterioration of the insulation failure and burnout of the stack and improve the safety performance of the stack.