According to the operating characteristics of a fuel cell power generation system, a fuel cell grid-connected control system model is developed. An active and reactive power control strategy for grid-connected inverter and a phase locked loop based on dual second order generalized integrator (DSOGI-PLL) are also designed. Under both the normal and the faulty three-phase voltage conditions, the simulation results demonstrate that the grid-connected control system can achieve unit power factor operation. Furthermore, the proposed DSOGI-PLL is able to detect the grid voltage frequency and phase quickly and accurately under one phase and two phase voltage faulty conditions, and is provided with adaptive frequency and filtering function. The correctness and validity of the proposed grid-connected system is also verified.