In order to explore the effects of afforestation on soil microbial community structures in the arid valley of Minjiang River, we selected different plantations with different cultivation years and site conditions to investigate soil microbial biomass and community structures by phospholipid fatty acids (PLFAs) method. The results showed that soil chemical properties were different among the types but not significant due to their short plantation time, while the soil microbial biomass increased significantly with the plantation time. For plantations with different site conditions, soil microbial biomass was higher in the plantation returned from farmland. The findings of above indicate that the response of microbial to environmental changes is more sensitive than that of soil chemical properties. Soil microbial biomass had significant correlation with soil total nitrogen content. It suggests that soil total nitrogen content is the key factor affects the soil microbial community structures in these plantations.