The content and the transmission characteristics of the water in the polymer electrolyte membrane fuel cell (PEMFC) have a significant influence on its performance. So far, there are few separate numerical studies on the process of water transport in the bionic flow channel, and the performance of bionic flow channel is different from conventional flow channel in part owing to the differences of their water drainage. Therefore, in order to understand the water drainage process of bionic flow channel, two different types of bionic flow channels are adopted in this paper. The method of numerical simulation is used to study the transmission process of liquid water in the bionic flow channel of different placement orientations. The simulation results found that the orientations of bionic flow channel has an influence on the process of water transport in the flow channel, and the process of water drainage also has a significant difference in the two different types of bionic flow channel.