Abstract: The community structure and energy flow process of artificial reef ecosystem are an important basis for scientific conservation and management of the artificial reef marine ranching. So far, there are few studies on the structure and the function evaluation of artificial reef ecosystems in tropical waters. In this context, based on the data of the annual fishery resources survey conducted in 2020, the Ecopath model of the artificial reef ecosystem on the east coast of Haikou was constructed, with 20 functional groups to quantify the trophic structure and phylogenetic characteristics of this ecosystem. Results show that the trophic level of each functional group in the artificial reef ecosystem on the east coast of Haikou ranged from 1.00 to 3.40, and the trophic level of the Sciaenidae functional group was the highest. The total flow of the system was 7538.807 t/(km²·a), of which 57.000% came from primary producers, and 43.000% came directly from the organic detritus. The energy flow path was primarily through the grazing food chain, and the overall conversion efficiency of the system was 6.266%. Cephalopods had the highest keystone index and relative total impact, which had a significant positive effect on medium and large carnivorous fish (0.57) and a significant negative effect on the saurida family (−0.77). The evaluation shows that the ratio of total primary production to total respiration was 3.494, the ratio of total primary production to total biomass was 119.244, the system connectivity index was 0.371, the omnivorous index was 0.311, and the Finn's cycle index and Finn's average path length were 7.833% and 2.476 respectively. It indicates that the system was in the not-yet-stabilized developmental stage, with a weak ability of resistance to external disturbances. It is recommended that, in the future, disturbance of the ecosystem by anthropogenic activities such as the construction of large-scale ocean engineering should be minimized, and the number of key species of higher trophic levels, such as cephalopods, ostracods, and medium- and large-sized carnivorous fishes, should be moderately increased, and the amount of phytophagous fishes harvested should be reduced, to increase the ecosystem trophic level and the efficiency of energy conversion, and to enhance the maturity and stability of the ecosystem in that sea areas should be increased.