A deteriorated water quality is closely associated with disease outbreak in aquaculture, where microorganisms play an indispensable role in water quality control and health of aquatic animals. To improve water quality, Rhizophora apiculata was planted in mud crab (Scylla paramamosain) farming. However, it is unclear whether and to what extent that R. apiculata plantation influences the gut microbiota and growth of aged mud crab. To address these concerns, we explored the bacterial communities of S. paramamosain gut and crab culture water at day 45, 114, and 132 after mud crab incubation under planting and non-planting R. apiculata. The results showed that R. apiculata plantation slightly increased the body weight of mud crab, and decreased the levels of total nitrogen, nitrite, ammonia, and salinity although the differences were statistically insignificant. Both bacterioplankton and gut bacterial communities were highly temporal dynamic, while the two communities were significantly distinct (ANOSIM r = 0.90, P = 0.0001). The relative abundances of dominant taxa in water and gut significantly varied between rhizophora and control group over mud crab aged. R. apiculata plantation promoted the diversity in gut microbiota, evidenced by more diverse core species. Further, R. apiculata plantation led to the dominance of Verrucomicrobiae lineages in water and Bacteroidetes and Lactobacillales members in gut, which are known probiotic members. A structural equation model revealed that water variables directly constrained gut microbiota, which in turn affected mud crab body weight (r = 0.52, P < 0.001). In addition, functional pathways involved in immunity, lipid metabolism increased significantly in rhizophora group, while those involved in infectious diseases exhibited an opposite trend. These findings greatly expand our understanding of the R. apiculata plantation effect on water quality, mud crab gut microbiota and their growth feature. Overall, R. apiculata plantation is beneficial for mud crab growth and health.