Global coastal zone is faced with the challenge of increasing threats from sea level rise, coastal erosion and storm surge as the result of climate change. To improve the adaptability of the coastal area to climate change, many scientists proposed to incorporate wetlands wave attenuation service into conventional coastal protection schemes, despite the knowledge gap of the spatial distribution of such service. In this study, we incorporated an exponential wave propagation model into GIS, and simulated the spatial distribution of the wave attenuation service of the coastal wetlands in Chongming island, Yangtze Estuary, under two normal scenarios (spring rise and neap rise). The results showed that coastal wetlands could reduce average significant wave heights up to 0.94 m and 0.54 m, accounting for 83.6% and 60.4% of their incoming wave heights under spring rise and neap rise, respectively. In either case, wave height reduced by the wetlands on the southern coast of Chongming island was lower than that on the northern coast. The spatial characteristics of wave attenuation rate was similar to that of the reduced wave height under neap rise. Compared to the neap rise scenario, wave attenuation rate of the wetlands along the southern coast of Chongming island showed a significant improvement under spring rise. The spatial heterogeneity of the wave attenuation service can be explained by the spatial patterns of coastal physical and biotic factors as well as their interactions. Not the whole transects of vegetation contributed to wave attenuation, even under spring rise scenario. Only a part of the transects, 70.8% in average, were engaged in wave attenuation under spring rise. This result indicates that the increased height of tide and wave may not induce the corresponding proportion increase in the width of ecosystem involved in dissipating waves due to the non-linear feature of ecosystems' wave attenuation service in space. This study can provide important support for coastal wetland restoration, ecosystem-based coastal management, and natural capital accounting.