Based on the ecological survey data of macrobenthos in the seagrass beds of Xincungang (2015~2016) and Li’angang (2017~2018) over four seasons, we compared the community structures. The results showed that: (1) A total of 96 species of macrobenthos were recorded in the seagrass beds of the two areas, with 50 species in Xincungang and 62 species in Li’angang, predominantly consisting of annelids in both seagrass beds. Dasybranchus caducus was a common dominant species. Except in autumn, the average inhabited density of macrobenthos in Xincungang was higher than in Li’angang, and except in summer, the biomass in Li’angang was higher than in Xincungang. (2) The Shannon-Wiener diversity index (H’), Pielou’s evenness index (J’), and Margalef’s richness index (d) in Li’angang were all higher than in Xincungang. The W value of the abundance/biomass curves (ABC) in Li’angang was much higher than in Xincungang, indicating that the macrobenthos community structure in the seagrass beds of Li’angang was more stable and less disturbed. (3) Based on the clustering results of community inhabited density and biomass, the communities in the two areas could be divided into two groups at a similarity level of approximately 15%, showing significant differences in the macrobenthos community structure in the seagrass beds of Xincungang and Li’angang. Combining these findings with historical research, the differences between the two communities are likely due to variations in hydrological characteristics and pollution from aquaculture activities. Compared with historical data, the macrobenthos communities in the seagrass bed protected areas of both locations have shown signs of recovery. Continuous protection and restoration efforts are effective and necessary.