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As the environmental considerations rise all over the world and under the drive of renewable energy policy, the society of hydrogen energy will come out gradually in the future. The proton exchange membrane water electrolyzer (PEMWE) is a very good hydrogen generator, characterized by low cost, high efficiency and zero emission of greenhouse gases. In this study, the micro temperature, humidity, flow, pressure, voltage, and current sensors were successfully integrated on a 50 μm thick Polyimide (PI) substrate by using micro-electro-mechanical systems (MEMS) technology. After the optimal design and process optimization of the flexible 6-in-1 microsensor, it was embedded in the PEMWE for a 500-h persistent effect test and internal real-time microscopic monitoring.