The Qinghai-Xizang Plateau (QXP), the highest plateau in the world, boasts a diverse array of ecological landscapes shaped by extreme climatic conditions; however, it is currently facing significant ecological challenges. In recent years, an increase in human activities, particularly the expansion of the human footprint and grazing intensity, has significantly exacerbated the pressures on habitat risk in the region. In this context, the future habitat risk trend under different scenarios on the QXP require further investigation. To address this gap, a comprehensive multi-scenario habitat risk prediction methodology was developed to fill this gap by integrating the InVEST model, the patch-generating land use simulation model, and the multilayer perceptron model, which combined land use and land cover data with human footprint index and grazing intensity data for a thorough assessment and prediction of habitat risk. Specifically, spatiotemporal changes in habitat risk on the QXP from 2000 to 2020 were analyzed, future indicators were projected, and spatiotemporal variations in habitat risk were evaluated under multiple scenarios. The findings indicate that high-risk areas experienced a significant increase of 39% in 2005; however, this was subsequently mitigated by protective measures. In the Ecological Protection scenario, high habitat risk was reduced by over 74%, while the Urban Development scenario saw an increase of 81% in high habitat risk. The alterations in habitat risks observed between 2005 and 2010 indicate that ecological conservation efforts on the Qinghai-Xizang Plateau have been effective. Among the various development pathways, the Ecological Protection scenario appears to be the most viable for the QXP. Nonetheless, the central and eastern regions of the QXP may continue to face an upward trend in habitat risk.