A fuel cell cooling system and a control method are provided. The fuel cell cooling system includes a fuel cell module having a fuel cell stack and a first cooling water line through which primary cooling water undergoing heat exchange with the fuel cell stack to adjust a temperature of the fuel cell stack circulates. A cooling module includes a second cooling water line through which secondary cooling water circulates and a cooling tower is configured to adjust a temperature of the secondary cooling water. A heat exchanger is connected between the first cooling water line of the fuel cell module and the second cooling water line of the cooling module for heat exchange. A controller configured to operate the fuel cell module and the cooling module.