High-energy proton microbeam facilities are powerful tools in space science, biology and cancer therapy studies. The primary limitations of the 50 MeV proton microbeam system are the poor beam quality provided by the cyclotron and the problem of intense scattering in the slit position. Here, we present an optical design for a cyclotron-based 50 MeV high-energy proton microbeam system with a micron-sized resolution. The microbeam system, which has an Oxford triplet lens configuration, has relatively small spherical aberrations and is insensitive to changes in the beam divergence angle and momentum spread. In addition, the energy filtration included in the system can reduce the beam momentum spread from 1 to 0.02%. The effects of lens parasitic aberrations and the lens fringe field on the beam spot resolution are also discussed. In addition, owing to the severe scattering of 50 MeV protons in slit materials, a slit system model based on the Geant4 toolkit enables the quantitative analysis of scattered protons and secondary particles. For the slit system settings under a 10-micron final beam spot, very few scattered protons can enter the quadrupole lens system and affect the focusing performance of the microbeam system, but the secondary radiation of neutrons and gamma rays generated at the collimation system should be considered for the 50 MeV proton microbeam. These data demonstrate that a 50 MeV proton microbeam system with a micron-sized beam spot based on a cyclotron is feasible.