In this experiment, the effects of different sources of phytase on growth performance, apparent digestibility of nutrients, and intestinal microflora of pigs were studied using feeding trial, digestion and metabolism trial and microflora test. A total of 144 weaner piglets (Duroc×Landrace×Large White) with the age difference less than 3 days, the same genetic background, similar body weight, and the same sex ratio were randomly divided into 4 groups with 6 replicates in each group and 6 piglets per replicate. The control group was fed a basal diet and experimental groups 1, 2 and 3 were fed the basal diet reduced 1/3 calcium monohydrogen phosphate supplemental level and added 500 (microbial source), 500 (tran-phytase-gene corn source), and 5 000 U/kg (tran-phytase-gene corn source) phytase to replace corn with an equal ratio, respectively. The experiment lasted for 90 days. The results showed as follows: compared with the control group, the average daily gain of experimental groups was higher (P>0.05) and that of experimental group 3 was the highest, and was increased by 1.85%; the average daily feed intake did not show a difference among all the groups; compared with the control group, the feed/gain of experimental group 3 was decreased by 1.49% (P>0.05). Compared with the control group, the apparent digestibility of dietary energy, crude protein, and crude fat of experimental groups did not significantly change (P>0.05), the phosphorus apparent digestibility of experimental group 3 was significantly increased (P<0.05) and the calcium apparent digestibility showed an improving trend (P>0.05). The phytase had no effect on the number of total aerobe, total anaerobe, Escherichia coli, Lactobacillus, and Bifidobacterium in ileum and cecum among all the groups (P>0.05). The results indicate that tran-phytase-gene corn source phytase and microbial source phytase in the diet of pigs have the same effect. With an increase in the dosage of tran-phytase-gene corn source phytase, the effect is more obvious. It has no negative effect on the growth performance and can reduce the calcium monohydrogen phosphate used amount and nitrogen and phosphorus emissions. Therefore, tran-phytase-gene corn source phytase can replace microbial source phytase in production practice.