Litters are the important component of forest ecosystem and play a key role in plant growth and ecosystem nutrient cycle. Soil microbial communities, as one of the driving factors of forest litter decomposition, can significantly influenced by forest litter composition. Understanding the responses of soil microbial communities to litters is of great significance to evaluate the influence of exotic species. We designed a simulation experiment with flowerpots to determine the impacts of exotic slash pine (Pinus elliottii) litter on the structure and function of soil microbial communities in comparison with the native masson pine (Pinus massoniana) litter at the Ecological Benefit Monitoring Station of the Yangtze River Protection Forest, which is located in Hengyang County of southern Hunan Province. The structure and function of soil microbial communities were determined by PLFA (phospholipid fatty acids) and BIOLOG (single carbon metabolism) methods, respectively at two stages (decomposition for 5 months and 18 months). The results showed that: (1) the initial carbon-nitrogen ratio of slash pine litters was significantly higher than that of native species masson pine. (2) Phospholipid fatty acids concentrations of soil bacteria and actinomyces under the slash pine litter treatment was significantly lower than those under masson pine litter treatment at the two stages. And at the latter stage (decomposition for 18 months), the phospholipid fatty acids concentration of fungi and the fungi-bacteria ratio of soil microbial community under slash pine litter treatment were significantly higher in comparison with masson pine litter treatment. (3) Microbial function diversity under the slash pine litter treatment was significantly lower than that of masson pine litter treatment: the carbon metabolic intensity, richness and diversity of soil microbial communities under the slash pine litter treatment were significantly lower than those under masson pine litter treatment at the early stages, and the carbon metabolic intensity and richness of soil microbial communities under the slash pine litter treatment also were significantly lower than those under masson pine litter treatment at the latter stages. (4) The structure of soil microbial community significantly affected its activity and functional diversity: The intensity and diversity of microbial carbon metabolism showed significantly positive correlations with bacterial phospholipid fatty acids. Characteristic phospholipid fatty acids concentrations of bacteria, 14 ∶ 0, 15 ∶ 0, a15 ∶ 0, i16 ∶ 0, 16 ∶ 1ω7c, a17 ∶ 0 and cy19 ∶ 0 significantly correlated with the intensity and diversity of microbial carbon metabolism. Our results suggested that slash pine litter significantly changed the structure and decreased the function of soil microbial communities in comparison with masson pine litter.