Estuarine wetland, where freshwater mixes with salt water, comprises different regions (rivers and marine ecosystems) with significantly varying tidal salinities. Two sampling areas, ZXS and JS, were selected to investigate the effect of tidal salinity on soil respiration (SR). ZXS and JS were located in Zhongxia Shoal and Jiangyanan Shoal of Jiuduansha Wetland respectively, with similar elevation and plant species, but significantly different in salinity. The results showed that with almost identical plant biomass, the SR and soil microbial respiration (SMR) of the tidal wetland with lower salinity (JS) were significantly higher than those of the tidal wetland with higher salinity (ZXS) (p < 0.05). However, unlike SMR and SR, the difference in the soil microbial biomass (SMB) was not significant (p > 0.05) with the SMB of ZXS a little higher than that of JS. The higher SMR and SR of JS may be closely connected to the soil microbial community structures and amount of dominant bacteria. Abundant β-and γ-Proteobacteria and Actinobacteria in JS soil, which have strong heterotrophic metabolic capabilities, could be the main reason for higher SMR and SR, whereas a high number of ε-Proteobacteria in ZXS, some of which have carbon fixation ability, could be responsible for relatively lower carbon output. Path analysis indicated that soil salinity had the maximum negative total influencing coefficient with SMR among the various soil physical and chemical factors, suggesting that higher soil salinity, restricting highly heterotrophic bacteria, is the principle reason for lower SMR and SR in the ZXS.