Currently, many constructed wetlands (CWs) are facing the threat of salinization, but its effect on the carbon sequestration function of CWs is still unclear. In this study, three CWs with different salinities (i.e., control: C-CW; low salinity: LS-CW; high salinity: HS-CW) were conducted. Increased salinity significantly reduced the carbon sequestration in CWs. The highest carbon sequestration was observed in C-CW (5.1 ± 0.2 kg C·m−2·y-1), and the carbon sequestration capacity of plants was identified as the major influencing factor. The substrate carbon pool decreased with salinity since it altered plant carbon inputs, enzyme activities, and microbial community structure. However, the decrement in the carbon pool management index with salinity indicated that salinity could enhance carbon pool stability and subsequently reduce carbon emissions of CWs. These findings improve the understanding in relationships between salinity and carbon sequestration in CWs and provide theoretical support for the proper management of CWs.