The Beijing-Tianjin-Hebei (BTH) mega-large urban agglomeration of China (CMUA) has significantly contributed to Chinese socioeconomic development. However, it faces severe shortages in the supply to meet the increasing demand of water, energy, and food resources (WEF). In order to safeguard the resource security of CMUA-BTH and the synergistic development of cities, and to compensate for the lack of dynamic analysis between urban agglomerations and WEF in previous studies. In this study, a coupled CMUA-WEF simulation model is developed based on the system dynamics approach. The model not only studies the three elements of WEF, supply and demand, but also conducts a comparative analysis of the three regions of BTH, and designs a total of four scenarios based on the possibility of future development, so as to facilitate the depiction of the trend of the WEF supply and demand system under different scenarios, and to provide theoretical basis for the government to formulate effective policy. The results show that: (1) Regarding demand, the aggregate demand for energy, food and water in the BTH will increase by about 3–5 times, 3 times, and 2 times, respectively, from 2000 to 2050, among which the total demand for energy will increase most significantly. In contrast, the variation of local resource supply side is small, which leads to the deterioration of resource security. (2) The risk of water shortage is the greatest in resource security, with less than 30% self-sufficiency in water security in all three regions. (3) Scenario analysis for CMUA-BTH indicates that "choking flow" (S3) yields more pronounced effects compared to "open source" (S2), and therefore adhering to the reduction of food waste, promoting energy-saving technologies, and intensifying water-saving measures can effectively reduce the risk of water shortages in the three regions. Optimal resource security in S4 increases Hebei's water pressure by 1.5%, alleviates Beijing's pressure by 7.3%, and the implementation of the Xiongan New Area and the new energy development policy can help realize the synergistic development of BTH and the inter-regional linkage.