A total of 320 ICR mice with body weight of (18±1) g were randomly divided into 4 groups, with 16 replicates in each group(half male and half female) and 5 mice in each replicate. The mice were fed with purified water(Pw), tap water(Tw), mountain spring water(Nw) and metasilicic acid mineral water(Mw), respectively. The mice were fed with maintenance feed. The pre-test period was 7 days and the test period was 90 days. After the test, the heart, liver, spleen, lung, kidney, brain and whole intestine of the mice were collected to determine the organ index. The orbital blood of the mice was collected to determine the serum biochemical indexes, and the cecal contents of the mice were taken to determine the relative abundance of intestinal flora. The effects of metasilicic acid mineral water on organ index, serum biochemical indexes and intestinal flora structure of mice were analyzed. The results showed that the intestinal organ index of mice in Mw group was 12.92±1.33, which was significantly higher than those in Pw and Tw groups. The conctentration of serum homocysteine(HCY) and plasma endothelin(ET) in serum biochemical indexes were (14.21±1.90) μmol/L and (105.63±10.10) ng/L, which were significantly lower than those in the other three groups. The conctentration of high density lipoprotein(HDL) in serum was (0.36±0.04) mmol/L, which was significantly higher than those in Pw and Tw groups. The mass conctentration of serum GLP-2 was (148.80±9.98) ng/L, which was significantly higher than that of Tw group. The Chao1 index of intestinal flora in Mw group was 337.20±21.89, which was significantly higher than that in Tw group. The relative abundance of Actinobacteria in Mw group was (10.20±3.28)%, which was significantly higher than that in Tw group. The relative abundance of Proteobacteria in Mw group was (1.67±0.18)%, which was significantly lower than that in Tw group. The relative abundance of Escherichia_Shigella and Enterococcus in Mw group were (0.38±0.05)% and (0.39±0.05)%, respectively, which were significantly lower than that in Tw group. The relative abundance of Desulfovibrio in Mw group was (0.87±0.06)%, which was significantly lower than that in Nw group. The relative abundance of Lactobacillus in Mw group was (27.64±2.15)%, which was significantly higher than that in Tw group. The relative abundance of Bifidobacterium in Mw group was (2.81±0.34)%, which was significantly higher than those of the other three groups. In summary, during the test period, mice drinking metasilic acid mineral water increased the whole intestinal organ index and serum high-density lipoprotein conctentration, reduced serum homocysteine and plasma endothelin conctentration, increased serum GLP-2 conctentration in mice, and increased the relative abundance of intestinal probiotics and reduced the relative abundance of mass intestinal pathogens. The changes in these indicators suggest that drinking metasilic acid mineral water may have a certain protective effect on the body.