This research alters the traditional single inlet/outlet opening of the pin type flow channel of direct methanol fuel cells (DMFCs). Multi-inlet/outlet openings are designed with the aim to distribute the methanol solution evenly and effectively remove CO2 bubbles and to improve the cell performance. The CO2 bubble dynamics in anode flow channels and the cell performance are investigated. Results show that the newly designed flow channels can overcome restrictions resulting from fuel and effectively remove CO2 bubbles, thereby enhancing the performance of the pin type DMFC. The “three-inlet and three-outlet” design increases the current density output by 19%.