The control and utilization of microorganisms in space-based animal culture constitute a pivotal challenge underpinning research domains such as space life sciences and extraterrestrial life-support system.This paper systematically examines the origins,transmission routes,and latent risks of microbial contamination in space-based animal culture facilities.A comprehensive analysis is conducted on the advancements in on-orbit implementation of microbial containment strategies,including physical filtration systems,antimicrobial surface coatings,and environmental parameter optimization.Additionally,the study evaluates the prospective applications of probiotic consortia and functionally engineered microorganisms in enhancing animal welfare,stabilizing biosphere conditions,and enabling closed-loop waste recycling.Notably,this work highlights the paradigm shift from reactive microbial suppression to proactive microbiome engineering in space-based animal husbandry,thereby establishing a theoretical framework for sustainable development of space-based animal culture.