In recent years, various countries have been paying attention to environmental protection issues, believing that climate change is the main challenge to the developed countries’ energy policies. The most discussed solution is renewable energy. The energy storage system can reduce the burden of the overall power system of renewable energy. The hydrogen energy is one of the optimal energy storage system options of renewable energy at present. According to these policies and the future trend, this study used micro-electro-mechanical systems (MEMS) technology to integrate micro voltage, current, temperature, humidity, flow and pressure sensors on a 50 μm thick polyimide (PI) substrate. After the optimization design and process optimization, the flexible six-in-one microsensor was embedded in the proton exchange membrane water electrolyzer (PEMWE) for internal real-time microscopic monitoring.