It is necessary to diagnose the flooding state of PEMFC in real time to ensure its long-term safe and efficient operation. However, the existing water flooding diagnosis methods still have many limitations, especially for the real-time monitoring of water flooding. Herein, a water flooding diagnosis method based on current density scanning is proposed, which can quantify the flooding severity and determine the flooding location by measuring the dynamic change of current density distribution. In this work, the current density distribution of a 50 cm2 single fuel cell is measured in situ using a current scan shunt (CSS) module with 256 current collecting segments, and the feasibility of this diagnosis method is verified by electrochemical impedance spectroscopy (EIS). The characteristics of serious flooding are explored under different load modes, and the results show that the voltage will decrease rapidly in a short time and there is a risk of electrode reversal under constant current mode; However, owing to the negative feedback effect, the severity of flooding under constant voltage mode eventually reaches a dynamic equilibrium. This work provides an effective evaluation method for water flooding diagnosis of PEMFC.