In early 2024, the primary oilseed rape production areas in the Yangtze River Basin experienced low temperatures and cold wave events, which severely impacted winter oilseed rape production. To investigate the effects of combined nitrogen (N), phosphorus (P), and potassium (K) fertilizer application on winter rapeseed yield and to examine the differential responses of rapeseed to these nutrients under freezing stress, a multi-site field experiment was conducted during the 2022/2023 (control year) and 2023/2024 (freezing stress year) growing seasons. The experiment included five treatments: no fertilizer application (CK), balanced application of N, P, and K (NPK), and treatments omitting nitrogen (–N), phosphorus (–P), or potassium (–K) based on the NPK treatment. By integrating meteorological data from the two growing seasons, rapeseed yield, yield components, shoot biomass, and harvest index were compared across multiple sites to analyze the response of rapeseed to freezing stress under different nutrient application conditions. The results showed that, compared to the NPK treatment, rapeseed yields in the –N, –P, and –K treatments were reduced by an average of 71.8%, 76.6%, and 13.4%, respectively, across the two growing seasons. This indicates that nitrogen and phosphorus fertilizers significantly improved rapeseed yield, while the effect of potassium fertilizer was comparably smaller. When comparing the freezing stress year to the control year, rapeseed yields were significantly reduced across all experimental sites. Specifically, yields under the CK, –N, –P, –K, and NPK treatments decreased by an average of 43.6%, 30.7%, 48.9%, 43.2%, and 45.7%, respectively. A lower number of siliques per plant was identified as the primary cause of yield reduction, with average decreases of 37.6%, 44.3%, 32.3%, 22.3%, and 22.8% observed in the respective treatments. Additionally, the number of seeds per silique and shoot biomass were significantly reduced under freezing stress, while the harvest index showed a significant increase. Further correlation analyses between rapeseed yield, climatic variables, and basal soil nutrient content revealed that the number of days with extreme low temperatures during the freezing period was positively correlated with the severity of freezing stress. Moreover, the nutrient demands for phosphorus and potassium intensified under freezing stress. In conclusion, nitrogen and phosphorus fertilizers are the primary nutritional factors contributing to high yield, while phosphorus and potassium fertilizers play critical roles in stabilizing yield under freezing conditions. A balanced application of N, P, and K fertilizers is essential for maintaining relatively high and stable yields in winter oilseed rape production.