Direct methanol fuel cells are a potential candidate to replace traditional power sources for portable applications. The flow field design, manufacture, and optimization are of great significance to the cell performance. When the scale of flow channels decreases to the level of submillimeter-scale, it is favourable to the reactant and product management. This paper focuses on the effectiveness of using a multi-tooth planing technique to create submillimeter-scale parallel channels in a graphite sheet. Besides the structural parameters of flow channels, a series of operating parameters are experimentally investigated, including methanol concentration, methanol feed rate, oxygen feed rate, cathode backpressure, and environmental temperature. Results indicate that the prepared channels promote a higher cell performance than the traditional design with a larger scale. It is beneficial to both the anode and cathode performances, but it has a more prominent effect at the anode. The methanol concentration of 4mol/L yields the best performance. Using a relatively lower methanol feed rate below 0.5mL/min has a more obvious effect on the fuel cell. The cell performance is insensitive to the change of cathode oxygen feed rate and backpressure especially when the oxygen can be sufficiently supplied. In this case we can use lower levels of oxygen feed rate and cathode backpressure. The cell temperatures and influence of environmental temperature are also discussed.