Human activities have impacted natural oyster reefs globally to varying extents, leading to a severe decline in the ecological functions of the majority of oyster reefs in China. In this study, we focused on the natural oyster reefs located in the typical intertidal zones of Longlou, Wenchang (on the east coast) and Haitou, Danzhou (on the west coast) in Hainan. Using the static model of Ecopath, we compared and analyzed the ecological structure and energy flow of these ecosystems. The study indicated that the trophic levels of the two oyster reef ecosystems were similar, the food webs were relatively simple, and the energy conversion efficiency of the first and second trophic levels were low, and both of them were dominated by debris food chain. The keystone functional groups include gastropods, arthropods, macroalgae and phytoplankton. The first trophic level faces an exceptionally intense predation pressure, with the amount consumed reaching up to 99.48% and 99.16% of the total predation, respectively. The majority of energy within these two ecosystems is concentrated at the first and second trophic levels, accounting for 99.88% and 99.67% of the total energy flow, respectively. In the Longlou oyster reef ecosystem, phytoplankton exhibit a stronger bottom-up effect, while the Haitou oyster reef ecosystem has a higher average energy transfer efficiency, reaching 7.046%. The connectance index (CI), system omnivory index (SOI), Finn's cycling index (FCI), Finn's mean path length (FML) and ascendency (A) of Haitou were 0.301, 0.111, 23.70%, 4.510 and 39.42%, respectively, which were higher than those of Longlou (0.281、0.110、9.927%、3.170 and 33.14%). The TPP/TR (total primary production/total respiration) and TPP/TB (total primary production/total biomass) value of Longlou are 2.442 and 6.557, respectively, while those of Haitou are 1.026 and 2.927, respectively, indicating that the oyster reef ecosystem in Haitou exhibits a higher degree of maturity and stability. Research findings indicate that the two natural oyster reef ecosystems possess a relatively high level of maturity and stability, with the oyster reef ecosystem in Haitou showing better health status than that in Longlou. However, both ecosystems are facing an issue where the energy transfer between the first and second trophic levels is impeded, with the majority of energy being directed towards detritus. This suggests a scarcity of organisms at higher trophic levels within the systems. Future management strategies should focus on reducing anthropogenic fishing activities targeting higher trophic level organisms such as nearshore predatory fish and crabs, to further enhance the stability of the oyster reef ecosystems.