Engineering disturbances are increasing in permafrost regions of northeastern China, where soil microorganisms play essential roles in biogeochemical cycling and are highly sensitive to linear infrastructure disturbances. However, limited research has addressed how microbial communities respond to different post-engineering-disturbance recovery stages. This study investigated the impacts of the China–Russia Crude Oil Pipelines (CRCOPs) on soil microbial communities in a typical boreal forest permafrost zone of the Da Xing’anling Mountains. Soil samples were collected from undisturbed forest (the control, CK); short-term disturbed sites associated with Pipeline II, which was constructed in 2018 (SD); and long-term disturbed sites associated with Pipeline I, which was constructed in 2011 (LD). Pipeline engineering disturbances significantly increased soil clay content and pH while reducing soil water content (SWC), soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) (p < 0.05). No significant differences in these soil properties were observed between SD and LD. Bacterial diversity increased significantly, whereas fungal diversity significantly decreased following pipeline disturbances (p < 0.05). The beta diversity of both bacterial and fungal communities differed significantly among the three disturbance types. At the phylum level, pipeline disturbance increased the relative abundances of Proteobacteria, Acidobacteriota, Actinobacteriota, Ascomycota, and Mortierellomycota while reducing those of Bacteroidota and Basidiomycota. These shifts were associated with disturbance-induced changes in soil properties. Microbial co-occurrence networks in SD exhibited greater complexity and connectivity than those in CK and LD, suggesting intensified biotic interactions and active ecological reassembly during the early recovery phase. These findings suggest that pipeline disturbance could drive soil microbial systems into a new stable state that is difficult to restore over the long term, highlighting the profound impacts of linear infrastructure on microbial ecological functions in cold regions. This study provides a scientific basis for ecological restoration and biodiversity conservation in permafrost-affected areas.