A manufacturing method of fuel cell having micro sensors and polymer layers is disclosed. It include the following steps of: (1) depositing first polymer layer step, (2) first lithographic processing step, (3) depositing chromium layer step, (4) depositing gold layer step, (5) removing first photo-resist layer step, (6) depositing second polymer layer step, (7) second lithographic processing step, (8) plasma etching step, (9) removing second photo-resist layer step, and (10) complete step. About this invention, the polymer layers can protect the micro sensors. The micro sensors can be installed at a specific location in the flow channel. The entire manufacturing cost is lowered.