This article introduces the instrument design of the medium energy proton detector (energy range: 30 keV–5 MeV) mounted on the FY-3E satellite. Through the design and optimization of the sensor signal processing circuit, the anti-electromagnetic interference ability of the medium energy particle detector is greatly enhanced. The designed aluminum plating on sensors can effectively exclude the light pollution to the medium energy protons. The designed permanent annular magnet has a deflection efficiency of more than 95% for medium energy electrons below 1.0 MeV. Additionally, by designing the logical working mode of the sensor, the contamination by other high energy particles (high energy electrons > 1.5 MeV, high energy protons > 5 MeV, and heavy ions) is excluded. Combining the above methods, the detector achieves the detection lower limit of 30 keV for medium energy protons. Its energy resolution is better than 15%@100 keV and the mixing ratio of electrons is less than 2%.