A cooling system of a fuel cell vehicle is provided. The cooling system includes a stack in which a plurality of fuel cells are laminated and a manifold in which the stack is disposed, and inside of which cooling water flows to exchange heat with the stack. Additionally, a flow control valve is installed in the manifold, and is opened and closed to exchange heat of cooling water with the stack based on a temperature of the stack. A cooling water flow channel then guides the cooling water into the inside of the manifold, and is dually arranged to exchange heat with the stack.