Synergies to achieve high phosphorus (P) use efficiency (PUE) and mitigate greenhouse gas (GHG) emissions are critical for developing strategies aimed toward agricultural green development. However, the potential effects of such synergies in the entire P supply chain through optimizing P management in crop production are poorly understood. In this study, a partial life cycle of a GHG emissions model was developed to quantify the P-related GHG emissions in the entire P supply chain in China. Our results showed that 16.3 kg CO2-equivalent (CO2-eq) was produced from the entire P supply chain per unit of P used for grain agriculture (maize, rice, and wheat). P-related GHG emissions in China increased more than five-fold from 1980 (7.2 Tg CO2-eq) to 2018 (44.9 Tg CO2-eq). GHG emissions were found to be strongly associated with the intensity of grain production in China, and they varied considerably across production regions owing to the differences in the P fertilizer production efficiency. Mineral P fertilizer use in crop production was the primary source of P-related GHG emissions. The results suggest that sustainable P management by matching mineral P fertilizer rates and fertilizer types with crop needs can mitigate GHG emissions by 10.8–27.7 Tg (24.0–65.1%). Moreover, this can improve PUE and reduce mineral P input by 0.7–1.4 Tg (24.0–46.0%). These findings highlight that potential synergies between high PUE and low P-related GHG emissions can be achieved via sustainable P management, thereby enhancing green agricultural development in China and other regions worldwide.