Abstract: Deteriorating sediment quality adversely affects the health of aquatic organisms and even threatens their survival. Sediment microorganisms, key drivers of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycling, are closely correlated with water quality changes in aquaculture systems. Yet, studies on the microbial community structure and function associated with sediment deterioration remain scarce. To explore the deterioration characteristics of the sediment during the culture of the swimming crab Portunus trituberculatus and their correlations with bacterial community, a 28-day crab culture was simulated in indoor canvas ponds using sea sand as the sediment. We monitored temporal changes in sediment appearance and physicochemical parameters. Using 16S rRNA gene amplicon sequencing, we profiled the sediment bacterial community, and applied redundancy analysis to examine its correlation with the physicochemical factors. Finally, we assessed functional changes via FAPROTAX and quantitative polymerase chain reaction techniques. The results showed that the color of sediment changed from initial grayish-brown to dark brownish-black, accompanied by the generation of an irritating odor. The shell color of swimming crabs changed from bluish-gray to yellowish-brown, and blackish-brown spots appeared on the surface of the shell and chelipeds, with the survival rate dropping to 38.1%. The temperature, pH, and dissolved oxygen content of the sediment continuously decreased, while the levels of ammonia nitrogen (NH₄⁺-N), unionized ammonia (NH₃), and nitrite nitrogen (NO₂⁻-N) first increased and then decreased, peaking at day14 and day 21, respectively. In contrast, the levels of nitrate nitrogen (NO₃⁻-N) and hydrogen sulfide (H₂S) continuously increased over 28 days. Meanwhile, the α-diversity of the sediment bacterial community first increased and then decreased, while the β-diversity exhibited three typical stage-specific characteristics: before deterioration (day 0), during deterioration (days 7–21), and after deterioration (day 28). Additionally, the dominant bacteria in the sediment shifted from Gammaproteobacteria to Alphaproteobacteria. The dynamic changes in the sediment bacterial community were driven by the synergistic effects of physical indicators such as pH and temperature, as well as chemical indicators such as H₂S and NH₄⁺-N. Functional analysis revealed that the nitrogen cycling functions (nitrification and denitrification) of the sediment bacterial community peaked at day 14 and day 21, with Nitrospira and Nitrospina being the main contributors to nitrification potential. In contrast, sulfur cycling functions significantly increased at day 28, with Desulfofaba, Fusibacter, Desulfovibrio, and other bacteria being the primary contributors to sulfur compound respiration. qPCR analysis revealed significant changes in the expression of 14 nitrogen-cycle and 4 sulfur-cycle functional genes during sediment deterioration, with nitrification (amoB and nxrA) and denitrification genes (nirK1-3 and nirS3) peaking at day 14, while sulfate reducing genes (dsrA, dsrB and aprB) peaked at day 28. These findings indicate that physicochemical indicators of the sediment and its bacterial community interact with each other, jointly driving the deterioration of the sediment. This study can provide basic data and theoretical references for the green and healthy aquaculture of P. trituberculatus.