Malignant weeds in agricultural lands spread more rapidly than normal weeds and are difficult to control effectively, thereby posing a severe threat to agricultural production. Identifying the current potential distribution areas of representative malignant weeds and their potential invasion of croplands under future climate changes are of great significance in the management of agricultural production. To predict the potential geographic distribution of the three malignant weeds, namely Avena fatua L., Poa annua L., and Setaria viridis (L.) P. Beauv., within the range of Qinghai-Tibet Plateau and to assess their invasive risk to cropland, we used an ensemble modeling approach, which comprised six algorithms: the generalized boosting model (GBM), artificial neural network (ANN), maximum entropy (MAXENT), random forest (RF), generalized linear models (GLM), and multivariate adaptive regression splines (MARS). The future climate change scenarios were described by four shared socioeconomic pathways (SSPs) for 2050a under the framework of CMIP6. Currently, the suitable area for A. fatua is 359 120 km², mainly in southwestern Sichuan and eastern Qinghai, with sporadic distributions in Gansu, Tibet, and Xinjiang. P. annua and S. viridis were predicted to have suitable areas of 430 460 km² and 200 360 km², respectively, primarily in southwestern Sichuan and southeastern Tibet, with scattered distributions in eastern Qinghai and southern Gansu. Mean annual temperature had the largest effect on the distribution of A. fatua, P. annua, and S. viridis. Subsequently, the human footprint index and soil available nitrogen were the dominant factors affecting the distribution of A. fatua, whereas soil pH and precipitation in the warmest quarter were relatively important for P. annua. Temperature seasonality and precipitation in the warmest quarter were the two significant factors in the distribution of S. viridis. By 2050a, under the four SSP scenarios, all three weeds showed different degrees of simulated expansion. The expansion area showed an increasing and then decreasing trend with increasing radiation forcing, except for S. viridis, which was expected to increase and then stabilize in the area. The proportion of potential distribution areas was consistent with the trend of weed expansion areas, and the proportion of main grain-producing areas was higher than that of non-main grain-producing areas. Under several future climate change simulations, the suitable area of the three malignant weeds would expand, which would lead to a higher invasion risk to cropland, especially in areas of main grain production. This study suggests that more efforts should be made in the future to focus on the physiological ecology, migration process, and control techniques of these malignant weeds in the main grain-producing areas of Qinghai-Tibet Plateau.