Compared with the normal environment, the microbiota in controlled closed cabins such as space capsules, Lunar/Mars bases have changed. To ensure the health of crewmembers, it is necessary to understand the effects of these changes on human symbiotic microorganisms and immunity. In this study, the experimental platform Lunar Palace 1 with a similar closed and controlled environment was used to research the effects of changed microbial exposure on human saliva microbiota and salivary cytokines. This paper studied on four crewmembers who participated in the third phase of the Lunar Palace 365 experiment, analyzing the dynamic changes of saliva microbiota and salivary cytokines, and further studying the correlation between salivary cytokines and highly abundant genera. According to our data, the crewmembers saliva microbiota and salivary cytokines fluctuated smoothly throughout the whole experiment. Although a part of microbes increased or decreased some times, they recovered quickly after leaving the controlled environment. The level of IL-6, IL-10 and TNF-α; in crewmembers saliva decreased from normal environment to the controlled environment, showing reduced levels of oral inflammatory response in crewmembers. In addition, although there were significant individual differences in crewmembers saliva microbiota, sharing living space reduced the difference. Furthermore, the level of TNF-α; showed a consistent positive correlation with the abundance of Actinomyces and Rothia in the controlled environment, indicating healthy individuals oral mucosal barrier may be sensitive to changes in saliva microbiota. According to the result, semi-sterile environments in controlled closed cabins did not cause persistent changes in human saliva microbiota and oral immunity. Besides, it provides a new idea for future research on the impact of the controlled environment on crewmembers health, and provides guidance for studying the effect of semi-sterile environments on human immunity based on saliva microbiota.