In China, the invasion of Spartina alterniflora is an important driver for the decrease of mangrove area and ecological service functions related to this habitat. In the past few decades, S. alterniflora clearing and mangrove restoration projects have mainly focused on the areas where it is already changed but ignored the potential distribution areas. This study suggested that implementation of mangrove protection prior to the areas with the threat of S. alterniflora invasion could greatly improve protection efficiency and save costs. Thus, using Maximum Entropy Modeling (MaxEnt), we estimated the potential spatial distribution of both mangroves and S. alterniflora in China, considering the current distribution data, topographical, sediments, sea surface temperature and bioclimatic variables. What’s more, we identified and calculated the potential distributed areas in each province. We aimed to explore (i) the key factors determining the distribution of mangrove and Spartina alterniflora along the coastline and (ii) the hotspots of their competitive occurrence, including S. alterniflora invasion areas and mangroves degradation areas, in order to support mangrove conservation. The model showed that the distance to the coastline and the topography play important roles in the distribution of S. alterniflora, while mangroves were more sensitive to the range of the annual sea surface temperature. Our results furthermore confirm that S. alterniflora has a wider potential distribution area (~10,585 km²) than mangroves (~9124 km²) at the coastline of China; and predict the provinces Zhangzhou, Quanzhou, Zhanjiang, Beihai and Wenzhou as hotspots for the competition between mangroves and S. alterniflora. We propose that priority should be given to the protection or restoration of mangrove plants in those areas which are co-suitable for mangroves and S. alterniflora. In these areas, management measures should be conducted that hinder S. alterniflora invasions or clear existing S. alterniflora plants, firstly. This study provides guidance for the management of native species by preventing biological invasion.