In this study, pot experiments were conducted on the seedlings of Pinus sylvestris var. mongolica to study the influence of Trichoderma (Trichoderma harzianum E15) and Ectomycorrhizal fungi (Suillus luteus N94) on the growth of these seedlings. In particular, the effects of these fungi on the fungal community structure in the rhizosphere soil of the seedlings were investigated. Inoculation with Trichoderma harzianum E15 and Suillus luteus N94 significantly (P < 0.05) promoted the growth of the Pinus sylvestris seedlings. The non-metric multidimensional scaling (NMDS) results indicated a significant difference (P < 0.05) between the fungal community structures in the rhizosphere soil of the annual and biennial seedlings. In the rhizosphere soil of annual seedlings, the main fungi were Ascomycota, Basidiomycota, Zygomycota. Ascomycota, Basidiomycota, Mortierellomycota, and p-unclassified-k-Fungi were the main fungi in the rhizosphere soil of biennial seedlings. The dominant genus in the rhizosphere soil and a key factor promoting the growth of the annual and the biennial seedlings was Trichoderma, Suillus, respectively. Both of them were negatively correlated with the relative abundance of microbial flora in the symbiotic environment. Trichoderma had a significant promoting effect on the conversion of total phosphorus, total nitrogen, ammonium nitrogen, nitrate nitrogen, and the organic matter in the rhizosphere soil of the seedlings, while Suillus significantly promoted the conversion of organic matter and total phosphorus.