Abstract: Water, energy, food, and forests are critical strategic resources necessary for sustainable development of the Yangtze River Basin (YRB). It is essential to examine the interconnected relationships among these four elements to achieve sustainable regional resource management. This study investigated the coupling mechanism of the water-energy-food-forest (WEFF) system in the YRB, as well as its spatial and temporal evolution in coordinated development, which significantly contributes to the high-quality development of the YRB and promotes Chinese-style modernization. This study analyzed the coupling and coordination development mechanisms in the WEFF system. Based on this, methods such as the comprehensive evaluation index model, coupling coordination degree model, and global spatial autocorrelation were employed to assess the comprehensive evaluation index, coupling degree, and coupling coordination degree of the WEFF system in the YRB from 2003 to 2021. Furthermore, the spatiotemporal characteristics were analyzed, and the grey prediction GM (1, 1) model was used to forecast the development trajectory for the next five years. The primary findings were as follows. 1) Regarding changes in the time series, the comprehensive evaluation index of the WEFF system in the YRB exhibited an unstable state, with an overall trend showing a gradual increase. The degree of coupling initially increased and then decreased, with all coupling stages occurring during the running-in stage. Similarly, the coordination degree of coupling showed an initial increase followed by a decline, and the type of coupling coordination changed from an imminent imbalance to barely coordinated. 2) In terms of spatial differences, the comprehensive evaluation indices of the WEFF system and the four subsystems in each province (municipalities) within the YRB were moderate (<0.7). Analysis of the comprehensive evaluation index of the WEFF system revealed that Qinghai Province recorded the highest indices overall, and Jiangsu Province ranked the lowest in the entire system. Among the subsystems, the water, food, and forest subsystems of the Qinghai Province exhibited the highest indices, whereas the energy subsystem of the Sichuan Province had the highest indices. Conversely, the water, energy, food, and forest subsystems of Shanghai Province were the lowest. The coupling degree of the WEFF system was not high; it was predominantly situated in the running-in stage with medium coordination, but with significant differences. Most provinces (municipalities) exhibited imminent imbalance, barely coordination or primarily coordination stages. Over most years, there was noticeable spatial clustering in coupled coordination, although the distribution pattern was unstable. 3) Regarding development simulation, the coupling coordination development status of the WEFF in the YRB from 2022 to 2026 closely resembled the developmental trend observed from 2003 to 2021, with variations among provinces (municipalities) within the basin. Therefore, this study proposed the following policy recommendations to enhance coordination among systems with high-quality development in the YRB. 1) Ensure that ecological protection aligns with the advancement of economic and social development, promoting the ecological restoration of the Yangtze River to facilitate a comprehensive green transformation of economic and social development. 2) Establish a cross-regional comprehensive negotiation mechanism to rationally determine functional positioning and development directions, leverage the industrial location advantages of diverse regions, and enhance coordination and cooperation of resources across regions. 3) Enhance cross-departmental communication and negotiation mechanisms for coordination between policy and practice while actively guiding the efficient and rational allocation of water, energy, food, and forest resources.