The impact of invasive species and land use change on soil nitrogen pools in coastal wetlands has been reported at local scale, but uncertainty persists for regional pattern due to geographical variability and limited field data. This study measured the top soil (upper 20 cm) organic nitrogen (SON), inorganic nitrogen (SIN) and total nitrogen (STN) concentrations and stocks across 21 coastal wetland sites in China (20°42′N-31°51′ N) that had undergone the same sequence of transformation from mudflats (MFs) to invasive Spartina alterniflora marshes (SAs) then to earthen aquaculture ponds (APs). Results showed that the conversion of MF to SA significantly increased SON and SIN concentrations and stocks by 37.7–86.1%, but subsequent conversion to APs significantly decreased them by 13.5–34.6%. SON/SIN ratio decreased upon invasion by S. alterniflora and it had a negative effect on STN accumulation, whereas conversion of SAs to APs showed the opposite trends. The change rates of SON, SIN and STN stocks showed clear decreasing trends with increasing latitude in the MF-to-SA conversion scenario, reflecting the strong influence of environmental temperatures, but weaker or insignificant trends were observed in the SA-to-AP conversion scenario, likely because of mitigating anthropogenic activities in aquaculture ponds. Our findings can be used to inform strategies to control invasive species and reduce the greenhouse gas nitrous oxide (N₂O) emissions, and support global N model for climate change in response to habitat modifications in coastal wetlands.