Although tidal wetlands in the Yangtze River Estuary are important carbon sinks, some are modified by different engineering measures to protect beaches, prevent corrosion, and promote tidal flat siltation. Nevertheless, some basic characteristics of these modified wetlands are still retained for their ecological service functions. Elucidation of the differences in carbon sink capacity and carbon storage of different types of modified tidal wetlands and the underlying reasons can provide theoretical guidance and a scientific basis for the protection and rational utilization of tidal wetlands, so as to maintain and enhance their carbon sink capacity. In this study, five typical modified tidal wetlands in the Yangtze River Estuary, namely, enclosure coastal wetland with Spartina alterniflora (ECS), enclosure coastal wetland with Phragmites communis (ECP), siltation coastal wetland with S. alterniflora (SCS), rock rip-rap riverside wetland with P. communis (RRP), and reclamation riverside wetland with P. communis (ReRP), were selected as study zones, and their carbon sink capacity and carbon storage were evaluated by analyzing soil organic carbon density, plant carbon fixation, and soil CO2 emissions. The possible reasons for the differences among these modified wetlands were considered based on elevation, average waterlogging time, tidal salt content, and vegetation types. The results showed that all the modified wetlands were net carbon sinks, with SCS exhibiting the highest carbon sink capacity (8.34–8.52 kg CO2 m− 2 year− 1), reaching the level of natural wetland, owing to its higher plant biomass and lower soil respiration intensity, followed by ReRP (2.68–3.15 kg CO2 m− 2 year− 1), ECP (2.56–3.37 kg CO2 m− 2 year− 1), RRP (2.94–3.04 kg CO2 m− 2 year− 1), and ECS (1.24–1.86 kg CO2 m− 2 year− 1). ReRP (26.89–27.82 kg CO2 m− 2) with long carbon accumulation history and SCS (24.57–28.6 kg CO2 m− 2) with high annual carbon sink capacity presented higher carbon storage (< 40 cm), followed by RRP (22.52–24.97 kg CO2 m− 2), ECP (16.14–18.18 kg CO2 m− 2), and ECS (5.74–6.70 kg CO2 m− 2). The difference in waterlogging time caused by diverse elevation, salinity, and vegetation types significantly affected soil respiration and plant carbon fixation, thus impacting CO2 emission and carbon sink capacity of different modified tidal wetlands. `