Antibiotics and heavy metals are potential pollutants that threaten the healthy development of coastal aquaculture. In this study, we conducted an indoor experiment using sediment column to evaluate the effects of sulfadiazine (SDZ) and plumbum (Pb2+) on nitrogen cycling of the sea cucumber Apstichopus japonicus culture pond system. Three treatments were designed i.e. SDZ treatment (SDZ), ion Pb2+ treatment (Pb) and the mixture of SDZ and Pb2+ (SP) were added to the overlying water of the sediment column. The fluxes of ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3--N) and nitrite nitrogen (NO2--N) in sediment-water interface; the gene abundance of ammonia monooxygenase (amoA), nitrite reductase (nirK, nirS) and nitrous oxide reductase (nosZ) in the sediments were evaluated; the sediment microbiota was analyzed by 16S rRNA. The results showed that three treatments all promoted NH4+-N emission; the emission of NO3-N and NO2-N were first decreased then increased in the three treatments(P<0.05). The sediment genes abundance were all significantly decreased in the three treatments, except that amoA in the SDZ treatment and nirS in the SP treatment were significantly increased(P<0.05). A total of 110 phyla in sediment microbiota were identified. The number of operational taxonomic units (OUTs) and Shannon index were significantly increased in the Pb and SP treatments(P<0.05). The functions of nitrous oxide reduction, nitrate reduction and nitrite denitrification microbial community acted as biomarkers which may influence nitrogen cycling process in sea cucumber culture pond. Difference abundance of microflora Proteobacteria and Firmicutes may influence the abundance of nitrogen cycling. In conclusion, the SDZ and Pb had an influence on nitrogen cycling emission of the sea cucumber culture pond system by changing the abundance of sediment microbial community and the nitrogen cycling genes. This study provide theoretical basis for optimizing the culture environment of sea cucumber from the aspect of nitrogen cycling.