AIM: To investigate the effects of on ocular surface microbiota in patients who received intravitreal injections. METHODS: Samples of ocular surface microbiota were obtained from 41 eyes of 41 patients who visited the Department of Ophthalmology. Patients were separated for three groups. Group A did not receive perioperative managements or intravitreal injection. Group B1 received only once and B2 received more than twice. In operating room, the samples were collected on the ocular surface. Operating taxonomic units (OTUs) clustering and alpha/beta diversity analysis was performed. The microbial 16S rRNA from samples were analyzed using the HiSeq 2500 platform. RESULTS: Alpha diversity did not differ in each group, and beta diversity differed in the B2 group. Beta diversity showed a significant difference between Group A and B2 (P=0.048). With the perioperative managements before intravitreal injection, the composition and relative abundance were altered. Top 10 microbiota on phylum and genus level, and then microbiota notably changed at genus level were listed. Gram-negative bacteria were varied more. Furthermore, Proteus was not found in Groups A and B1, but it was appeared after the patients received perioperative management and intravitreal injections in Group B2. CONCLUSION: With the perioperative managements, the balance of microbiota on the ocular surface is destroyed, and relative composition and abundance of microbiota on the ocular surface is obviously altered. The clinical doctors should pay more attention on the consequence of perioperative managements before intravitreal injection.