Abstract Large‐scale restorations being implemented in coastal China involve replacing invasive Spartina alterniflora with mangroves, yet the full effects of such saltmarsh‐mudflat‐mangrove land‐use change on the blue carbon sink are largely unknown. This study, using paired eddy covariance measurements of greenhouse gases (GHGs) before and after S. alterniflora removal, reveals that such restoration efforts through excavation and burial of S. alterniflora inadvertently cause pulse methane emission. The emission negates the carbon sink benefit and causes a significant climate debt, potentially taking over 3 decades to offset. These findings highlight the risk of GHG changes from coastal restoration in neutralizing potential blue carbon sink and call for refining current restoration practices to mitigate unintended environmental impacts. This has important implications for achieving climate benefits along with other ecosystem service co‐benefits in coastal restoration, particularly for China’s coastal wetlands where S. alterniflora removal is being implemented as the world’s largest ecosystem restoration effort.