Root-associated fungi exert ecological functions to affect the growth of host plants through complex interactions, but the complexity and stability of networks and the influencing factors remain unclear. To illuminate the complexity and stability of molecular network of root-associated fungi (RaF) associated Pinus sylvestris var. mongolica and investigate the environmental driving factors, we select natural forests and plantations (half-mature, nearly mature and mature forest) in the Hulunbuir Desert, Horqin Desert, and Mu Us Desert to determine RaF network by using molecular ecological network analysis. The results indicate that 1) The interactions of RaF are dominated by positive correlation and there is stronger competition among fungi in natural forest; The complexity of RaF network in plantations is higher than natural forest, and RaF network in the Mu Us Desert is the most complicated; With the stand aging, the complexity reaches the maximum in nearly mature plantation. 2) Ascomycota is the main key fungi flora. The main genera are Inocybe, Calostoma, Cladophialophora and so on. Saprophytic closely contact with others in plantation and natural forest, but pathotrophic fungi appear as keystone in plantation forest. 3) Compared with plantations, RaF network of natural forests has higher stability, and the stability of RaF network of Horqin Desert is higher than others. In different deserts, the stability reaches the maximum in the half-mature plantation. 4) Complexity of RaF network is significantly correlated with mean annual temperature, mean annual precipitation and soil nutrient, but there is no significantly correlation between stability of network and environmental factors. In conclusion, the environment and stand ageing shape the variation of RAF network complexity and stability. The stronger stability in natural forests is beneficial to forest growth. Plantations meet the growth demand through more complied network. Saprophytic closely contact with others, but pathotrophic fungi may have negative effect on the growth and health of plantations.