Given the high power density and environmentally friendly, e.g. low emission and noise, proton exchange membrane fuel cells (PEMFCs) have been considered to be promising in applications to transportation, combined heat and power (CHP) systems and portable electronic devices.^[1-4] Therefore, new strategies are highly demanded to keep promoting the performance enhancement and device integration in more compact manner. In this work, novel designs of the miniature flow fields and integrated PEMFCs were realized on Si wafers. In order to maintain the good mass/electron transfers for sufficient and efficient electrochemical conversion of the fuel, the vertical dot-type flow fields were fabricated by template-assisted dry etching cooperating with the dicing and deposition of Cr/Au conducting layers. Eventually, the integrated Si-based PEMFC were constructed by combining the commercial Pt/C catalysts (the load of Pt was 0.2 mg/cm²) and carbon black as gas diffusion layer (GDL) within the Si-based flow fields, in which a highest peak power of 354 mW/cm² was accomplished. This work proposed a unique design and Si-compatible processing of the integrated FCs, which may present potential industrial applications.