In arid regions, agricultural expansion often triggers environmental degradation through complex pathways. However, the key system mechanisms remain unclear, which hinders targeted management. This study proposed the hypothesis that cropland expansion drives ecological environmental change by disrupting system coordination, and took Aksu River basin as typical area. We adopted the pressure-state-response model and the optimized self-organizing feature mapping model to reveal the spatial differentiation pattern of ecological vulnerability (EV), and then used the coupling coordination degree (CCD) model to analyze the evolvement mechanism of coordination. Finally, the mediation effect analysis was used to explore the dynamic correlation path between CCD and EV, and the moderating effect of climate. The results showed that the EV of mountain zone was directly affected by the expansion of cropland on forests. However, the vegetation degradation in the oasis-desert transition zone was mainly caused by the unreasonable allocation of water resources, and the grassland degradation in the desert zone was mainly caused by cropland occupation, which led to the increase of EV. In contrast, the EV in the oasis zone was mainly directly driven by human activities and weakly correlated with CCD. Warming temporarily increased water from glacier melt but intensified evapotranspiration, threatening sustainable oasis agriculture. Therefore, dryland agriculture management should shift towards coordinated development among agriculture, water resources and vegetation, rather than being confined to single-factor control such as irrigation water. This framework provided scientific basis for differentiated governance of dryland agriculture by identifying the correlation mechanisms between system coordination and EV.