Microbes in coral reef sediments are thought to play an important role in organic matter remineralization and nutrient recycling. Microbial communities also reflect the environmental conditions, such as nutrient status, of an ecosystem. This study investigates the relationship between microbial community diversity in the reef sediments and environmental conditions at Liuqiu Island. We sampled sediments seasonally from four sites around the island, Beauty Cave, Geban Bay, Houshi Fringing Reef, and Lobster Cave, from 2015–2020. The V5–V6 hypervariable region of 16S rRNA was amplified and sequenced using the Illumina MiSeq platform to identify the microbial communities. The results showed that the high abundance of Pseudomonadota, Planctomycetota, and Bacteroidota might reflect the eutrophic environments of the sediments on Liuqiu Island. Second, the identification of putative pathogens and human-related genera suggests that human activities have affected the marine environment of Liuqiu Island. Third, the insignificant spatial differences and the significant temporal differences in the microbial communities of Liuqiu Island indicate that annual or periodical events, such as the Kuroshio Branch Current and South China Sea Surface Current, could shape the microbial communities of Liuqiu Island. Furthermore, the abundance of human-related genera—Cutibacterium, Herbaspirillum, Corynebacterium 1, Escherichia-Shigella, and Kocuria—increased dramatically in the Lobster Cave site in September 2015 and may have been induced by a strong climate event, such as a typhoon or heavy rainfall. Our results revealed that the microbial communities of Liuqiu Island are dynamic and sensitive to adjacent environmental conditions. The sedimented microbial communities could monitor the bacteria and pathogens related to human activities and even reveal the putative events that could affect the ecological environments.