A fuel cell with bipolar plates having micro channels and its manufacturing method are disclosed. The structure of this fuel cell includes a pair of bipolar plates and a catalytic portion. The bipolar plate has a gas inlet, a gas outlet, a main channel, several blocking portions, and many micro channels formed on the blocking portions and connecting two adjacent sections of the main channel. The manufacturing method includes (1) preparing step, (2) first-layer structure manufacturing step, (3) second-layer structure manufacturing step, and (4) complete step. It can increase the gas contacting area. It can drain off water more effectively. It is suitable for mass production.