The temperature and flooding phenomenon during operation can strongly influence a proton exchange membrane fuel cell (PEMFC) performance. Non-uniform conditions exist in each segment of fuel cell. Previous studies have investigated these conditions on the mm scale using destructive methods or simulation, but none has been able to obtain exact data from within the fuel cell. This research applies micro-electro-mechanical systems (MEMS) to develop a flexible micro temperature, pressure and flow sensor. It is composed of main two parts: 1. Fabrication of flexible micro sensors on polyimide (PI) film by MEMS; 2. Embedding flexible micro sensors into a PEMFC for in-situ diagnosis and performance. Internal temperature data demonstrate that the downstream exceeds upstream and midstream, because the generated heat is carried by gas from the inlet and downstream, where it undergoes a severe reaction. Monitoring the inner pressure for a long period revealed that the accumulation and elimination of water in flow field may be responsible for increased pressure and the recovery. The flow rate that is supplied by the flow controller in the testing system exceeds those measured by the upstream and downstream sensors. This deviation is consistent with the results of a fuel cell leak test. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.