Background Accompanying its rapid economic development and population growth, China is the world's third largest acid rain region, following Europe and North America. The effects of acid rain on forest ecosystem were widely researched, including the growth, the nutrient of the leaf and soil, and so on. However, there are few reports about the effects of acid rain on the soil microbial diversity. This study investigated the effects of acid rain on soil microbial community function under potted Masson pine seedlings (Pinus massoniana Lamb). Results After 7 months of treatment with simulated acid rain, the low acid load treatment (pH 5.5) stimulated soil microbial activity, and increased soil microbial diversity and richness, while the higher levels of acid application (pH 4.5, pH 3.5) resulted in lower soil microbial activity and had no significant effects on soil microbial diversity and richness. Principal component analysis showed that there was clear discrimination in the metabolic capability of the soil microbial community among the simulated acid rain and control treatments. Conclusion The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.