Abstract: Research on the ecological impacts of Spartina alterniflora invasion was conducted by comparing the benthic macro-invertebrate communities in S. alterniflora salt marsh and bare flat habitat in Qingshantou Estuary, Beihai City, Guangxi Zhuang Autonomous Region. The results showed that:1) Fifteen macro-invertebrate species, belonging to Arthropoda, Mollusca, Annelida and Sipuncula, were collected in the two types of habitat from July 2012 to September 2013, in order to determine responses of macro-invertebrate communities in species composition, biomass, density and diversity towards altered living habitats induced by S. alterniflora invasion. Glauconome chinensis was the predominant species in the salt marsh, occupying 86.7% of the entire macro-invertebrate species population. Mictyris brevidactylus was the dominant species in the bare flat. 2) Based on two-way analysis of variance (ANOVA), the macro-invertebrate species population size increased with the invasion of S. alterniflora. Particularly, the population size of G. chinensis boomed, which was one of the causes of increasing macro-invertebrate species density and biomass under the invaded habitat. No distinguished difference of the Margalef, Shannon-Wiener, Simpson richness and evenness of macro-invertebrates was found across temporal and spatial scales. 3) Non-metric multidimensional scaling analysis showed that the community structure of macro-invertebrates in S. alterniflora habitat was similar to that of bare flat habitat in the different sampling times, though the similarity in fall 2013 was reduced compared to the fall from the previous year. The impacts of S. alterniflora on macro-invertebrate community might vary in future scenarios with longer invasion of S. alterniflora. In conclusion, the invasion of S. alterniflora increased the biomass, density and population size of macro-invertebrates in bare flats in Qingshantou Estuary, but it did not affect their diversity or the community structure.