A fundamental understanding of the water balance of a fuel cell during operation is crucial for improving the cell performance and durability. The humidification in the anode or cathode has an important effect on the flow characteristics and cell efficiency. Three-dimensional steady mathematical model based on the electrochemical, current distribution, fluid motion continuity equation, momentum and energy equation, boundary layer theory has been developed to simulate PEMFC with interdigitated flow field using the computational fluid dynamics (CFD). Effects on the current density and temperature differences have been simulated and analyzed respectively, when the humidification in the anode or cathode is from 0% to 100% respectively. The numerical results show that the humidification strongly influences the current density and temperature difference so as to affect the cell efficiency. Under the same operation conditions and low humidification conditions, anode humidification can better enhance the performance of the battery and improve the extent of PEM humidification.