Abstract Flooding experiments in various conditions are developed and the hydrogen pressure drop is investigated on a two-piece PEM fuel cell in this study. A two-level characteristic of hydrogen pressure drop is observed and analyzed in combination with water droplet accumulation in channels. Based on the characteristic, the flooding process can be divided into four continuous periods, which are the proper period, the humid period, the transitional period and the flooding period. The voltage shows the segmented tendency during these periods. Experimental results show that current and temperature have little influence on the growth rate of the two levels, while the effects of pressure and hydrogen stoichiometry are remarkable. The growth rate can be calculated through the channel dimensions and matches the experimental results well. Hydrogen purge is not a fundamental method to solve flooding. The end of the humid period should be the boundary before flooding. The moist section can be obtained in the beginning part of the humid period. In this section PEM fuel cell is neither flooding nor dehydration by adjusting the cell temperature, which is verified by two additional experiments. This water management is convenient and swift for PEM fuel cell applications and the fault diagnosis.