A system of a plurality of parallel-connected fuel cell converter devices and a method for controlling the system are provided. The system includes a plurality of fuel cell converter devices, a parallel connection unit, a power control unit, a Mux control unit, and a master controller. The output ends of the plurality of fuel cell converter devices are connected in parallel by the parallel connection unit. The master controller reads signals from the power control unit and the Mux control unit and determines accordingly which fuel cell converter devices need to be turned on to meet the requirement of a load. The method includes the steps of estimating a load, determining the number of the fuel cell converter devices to be turned on, calculating an output power, discharging, and charging. Thus, the plurality of fuel cell converter devices is controlled to output the required power of the load.