<sec>Proton is the main particle component in the space radiation environment. The proton single event effect cannot be ignored with the continuous development of semiconductor technology. Accelerator simulation is the most important method to evaluate the single event effect caused by proton radiation, and the accurate measurement of proton flux is the most critical aspect in the device evaluation process. The research is based on the 100 MeV proton single-event irradiation device of the Atomic Energy Institute, which breaks through the wide-range mid-energy proton fluence rate measurement technology. The detection tools are developed such as Faraday cup, plastic scintillator detectors and secondary electron emission monitors, which can be used for measuring the proton beam current in a wide range. Faraday cup and plastic scintillator detector can be used for measuring the high flux proton and the low flux proton, respectively. Secondary electron emission monitor can be used for conducting the online real-time measurement. The proton fluxes in a range of 10<sup>6</sup>– 10<sup>7</sup> p·cm<sup>–2</sup>·s<sup>–1</sup> are measured by using two separate detectors.</sec><sec>The analysis of the fluence rate uncertainty is carried out. The uncertainty of measurement results mainly include three aspects: measurement method, measuring instrument and equipment, and repeatability of multiple measurement results. Here in this work, the Faraday cup is taken for example to analyze the uncertainty sources in the proton flux measurement. The measurement methods include the calculation of the collection efficiency of the Faraday cup (collection efficiency + escape rate = 1) and the calculation method of flux (flux = current/collection area). For the measuring instruments and equipment, mainly including 6517A and other electronic devices, their errors are determined by the accuracies of the instruments themselves. Repeatability of multiple measurement results mainly from the error caused by the instability of the accelerator beam output, the error caused by randomness of multiple measurement results, and the error given by the statistical method. The analysis shows that the uncertainty of flux measurement by Faraday cup is 7.26%, and the uncertainty of flux measurement by plastic scintillator detector is 1.64%.</sec><sec>The flux measurement of the proton fluence rate has reached the level of similar devices in the world, filling the gap in this field in China. It has a certain reference and guiding significance for the follow-up study of medium- and high-energy proton beam measurement in China. The mid-energy proton flux measurement system and uncertainty analysis method established in this study lay the foundation for accurately evaluating the component radiation effects.</sec>