The intestinal microbiota is significantly affected by the external environment, but our understanding of the effects of extreme environments such as Antarctica is far from adequate. In this study, we selected five representative time points: living in Antarctica for 2 months (summer, T1), 5 months (before-wintering, T2), 8 months (mid-wintering, T3), 11 months (the end of wintering, T4) and 7 months after returning to China (T5), and compared the gut microbiota and clinical indexes. The results showed that the Antarctic environment has a profound impact on the intestinal microbiota and blood clinical indexes of individuals, and this effect may persist for quite a long time even after leaving Antarctic. The T5 group were also clustered near T4 instead of T1. Notably, T2, T3 and T4 are more clustered compared with the T1 group. At the phylum level, the main dominant bacteria in the population are Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria, with average proportions of 0.79, 0.12, 0.06, and 0.02, respectively, showing a western-style dietary microbiota composition. Compared with that in the T2, T4 and T5 groups, the relative abundance of Actinobacteria was significantly increased in the T1 and T3 groups. At the genus level, we found a genus with a step-like increase in the content of the genus-Alistipes, and it decreased significantly after returning to the normal environment. In the T2 group and T3 group, some clinical indexes such as TT4, ALT, UA, Scr, CysC, TC, HDL, APOA1 and APOB, their values are higher than T1, T4 and T5 group. This may be caused by cold and a diet based on meat. The probiotic, Pseudobutyrivibrio is negatively related to SCR, TC, LDL, APOB. The study will provide new research objects for mechanistic studies and intervention targets for Antarctic adaptation.