Abstract: The on-orbit manned spacecraft provides an optimal habitable environment with suitable temperature, humidity and air composition for crew members, as well as favorable conditions for the growth of microorganisms. Meanwhile, the special space environment including the microgravity and the radiation may aggravate the microbial corrosion capability. Therefore, the control and the protection of the space microbial effects should be systematically studied. The microbial control and protection system contains the following four aspects: the collection and the identification of space microbial strains, the microbial corrosion mechanism of the space materials in space, the choice of antimicrobial coated materials used for the manned spacecraft, and the system microbial protection both in orbit and on the ground. The results can serve as a reference for the study of the microbial control and protection technology for inflight manned spacecraft.