The invasion of Spartina alterniflora Loisel, a perennial herb that was introduced into China in 1979, has become an important environmental problem in coastal zones of Jiangsu Province. Although microorganisms play an important role in the structure of ecosystems, the effect of S. alterniflora on soil microbial metabolic diversity remains unexplored. In this work, the variations produced by S. alterniflora in the seasonal dynamics of soil microbial metabolism were examined and compared with the soil microbial metabolism of bare flat. The obtained results indicated that S. alterniflora increases soil total carbon content during the whole year, and decreases soil salinity in spring, summer and winter. The presence of S. alterniflora enhanced the metabolic activity of soil microbes in summer. In autumn, Shannon (H’) and Pielou (J) indices were significantly decreased in S. alterniflora-invaded soil. S. alterniflora altered microbial carbohydrate, amino acid, carboxylic acid, and phenolic acid metabolism in a season-dependent manner, and enhanced microbial amine metabolism during the four seasons. Redundancy analysis demonstrated that soil pH and salinity are driving the metabolic functional diversity in coastal wetlands. Taken together, these results confirmed that the invasion of S. alterniflora is modifying soil physicochemical properties and, subsequently, altering soil microbial metabolic diversity.