As a practical management approach to combat global warming, reforestation may affect microbial communities. However, the effects of Pinus thunbergii forest restoration on microbial colonisation and community structures in saline areas are poorly documented. Herein, microbial communities were investigated in two different pine stand age forests, in addition to bare sites, through Illumina MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA, and predicted using the PICRUSt2 and FUNGuild databases. The restoration of P. thunbergii shelter in saline areas caused significant changes in soil properties and microbial community characteristics. NMDS analysis exhibited significant differences in fungal and bacterial composition, as confirmed by the Adonis test (p = 0.04 and p < 0.01). Microbial communities were significantly affected by soil properties, with fungal and bacterial diversity being positively affected by soil's rapidly available-K (R = 0.15 and 0.22) and hydrolysable-N (R = 0.16 and 0.11). Of all guilds, endophytes and mycorrhizal fungi had a marked effect on specific bacterial compositions. The topologies of microbial networks showed that microbial network complexity was lower in low-growth forests, while stable below-ground microbial community structures could form under long-term P. thunbergii vegetation. During the restoration process, soil fungi were less susceptible to the vegetation successional stage, while soil bacteria were more sensitive. Over time, the diversity of bacteria and fungi was mainly driven by soil characteristics as well as the restoration of P. thunbergii. Further, forest restoration and mycorrhizal fungi could shape specific bacterial community compositions in saline soils.