The effect of siltation promotion and the agricultural utilization mode of the inning land on soil microbial respiration (SMR) in tidal wetlands of the Yangtze River estuary were investigated. Three typical zones in Chongming Dongtan and Jiuduansha, located near the Yangtze River estuary, were studied to determine the variability of SMR in natural and artificially disturbed wetland areas. The causes of the differences in SMR were also studied by analyzing microbial activity and physical-chemical characteristics of the different wetland soils. Results showed that the SMR of the existing wetland in the siltation promotion zone was significantly higher (P<0.01) than that of the natural zone. Different agricultural practices on the inning land also affected the SMR of the tidal wetlands. Higher soil microbial activity in the artificially disturbed tidal wetland may be the main cause of its high SMR. Path analysis indicated that the correlation between soil prokaryotic microorganism diversity, invertase activity and SMR were especially prominent. Siltation promotion and agricultural utilization of the inning land leading to a change in soil structure and characteristics of the existing tidal wetland, such as decrease of water capacity and increase of inorganic N, may be important reasons for the differences in soil microbial activities between the artificially disturbed and the natural tidal wetland. All of the results indicated that siltation promotion and agricultural production on the inning land would enhance SMR of the existing wetland, thus decreasing its carbon accumulation capability. The investigation provided useful guidance for wetland protection schemes and the better utilization of tidal areas in the Yangtze River estuary.