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MEMS-based micro direct methanol fuel cells (muDMFCs) have poor performance because polymer electrolyte membrane fuel cell (PEMFC) is not well compatible with MEMS process. In this work, fine pattern was formed on PEM using nanoimprint technology. Using the nanoimprint PEM, a MEMS-based muDMFC was fabricated. The MEMS-based muDMFC had the open circuit voltage (OCV) of 0.74 V and the maximum power density (MPD) of 0.2 mW/cm2, which were higher by about 2-7 and 10 times, respectively, than those of the state-of-the-art MEMS-based muDMFC with planar electrode. It demonstrated that the nanoimprint technology could help us to integrate PEMFC and MEMS technology into on-chip power application.