In recent years, the conflicts of the human–land coupling system (HLS) in the cross-border transportation corridor areas have become increasingly severe, especially in the China–Mongolia–Russia Cross-Border Transportation Corridor (CMRTC). The vulnerability assessment of the HLS-CMRTC is the key scientific issue for regional sustainable development. Based on the nearly 20 years of a scientific expedition, we set the CMRTC as the study area, constructed the vulnerability assessment index system and quantitative model, assessed the vulnerability of the HLS-CMRTC, revealed the key influencing factors, divided vulnerability risk prevention zones, and proposed the targeted optimization countermeasures. This study found that: (1) The overall vulnerability pattern of the HLS-CMRTC showed a vulnerability level gradually increasing from south to north. (2) Permafrost instability risk, land desertification, temperature increase, and backward social development were key influences. (3) Vulnerability risk prevention zones were divided into four priority and two general zones. The targeted optimization countermeasures were proposed, such as establishing an ecological security barrier, carrying out collaborative ecological risk monitoring, and early warning. The conclusions could provide a decision-making basis for the study area to reduce the vulnerability of the HLS. They could also provide reference and scientific support for achieving sustainable development of the economy and environment in similar regions of the world.