The integrated micro proton exchange membrane fuel cells (μPEMFCs) were fabricated by constructing the hierarchical dot-type flow fields on Si wafers and then being compacted with the carbon black as gas diffusion layer (GDL) and Pt/C catalyst layer, which presents the simplicity and good device-integrity by replacing the traditional carbon paper or cloth as GDL and omitting the hot-press processing. The Si-compatible processes, including the template assembly of SiO2 spheres, dry etching, channel dicing, were elaborately manipulated to optimize the wafer-scale hierarchical flow field and thus industriously improve the fluids transport and gas distribution. Ultimately, the peak power of over 1W/cm2 was accomplished when the graphite bipolar plates were replaced by the hierarchical Si-based flow fields alone, while the maximum power of 354 mW/cm2 was successfully demonstrated in the integrated Si-based μPEMFCs with measured size of 4 cm2. This work not only broadens the application of PEMFCs to micro/nano-electro-mechanical systems (M/NEMS) or other Si-based electronic devices, but also provides guidelines for fabricating other metal-air batteries such as Zn-air batteries and Al-air batteries.