The application of nitrogen (N), phosphorus (P), and potassium (K) fertilizers is an important measure to increase yield in agricultural production. Continuous upland and paddy-upland anniversary multiple cropping rotation is the main planting mode of winter oilseed rape in the Yangtze River basin in China. In order to explore the effects and differences of N, P, and K on the yield and nutrient absorption and utilization of rapeseed in different rotations, a field experiment was carried out in Shayang County, Hubei Province for 3 years from 2017 to 2020. Two rotation modes of upland-oilseed rape (maize-rape) and paddy-oilseed rape (rice-rape) were adopted, and four treatments of nitrogen, phosphorus and potassium combined application (NPK), no nitrogen (-N), no phosphorus (-P), and no potassium (-K) applications on the basis of NPK were set in each rotation. The yield, yield components, and nutrient uptake of rapeseed were analyzed, the fertilizer use efficiency and soil indigenous nutrient supply were evaluated. The average results of the three-year trials showed that, compared with the NPK treatments, the -N, -P, and -K treatments in upland reduced rapeseed yields by 68.4%, 89.6%, and 7.0%, and by 71.0%, 84.7%, and 6.4% in paddy fields, respectively. Among the yield components, whether it was upland or paddy, fertilization had the greatest impact on the number of siliques, followed by the number of grains per silique, and had the least impact on the thousand-grain weight. Compared with NPK treatment, the number of siliques in upland and paddy fields was decreased by 61.6% and 52.0%, 82.0% and 67.8%, 16.2% and 19.7% due to N, P, and K deficiency, respectively. There were significant differences in the yield and nutrient absorption of rapeseed in upland and paddy field under different fertilization treatments. The yield of rapeseed in upland was about 27.2%, 15.2%, and 16.7% higher than that in paddy field in the -N, -K, and NPK treatments, while the yield of paddy rapeseed under -P treatment was 20.8% higher than that of upland. Nutrient accumulation trends were similar to the yield, except for -P treatment, the accumulation of N, P, and K in the upland oilseed rape under NPK treatment was 20.4%, 37.3%, and 4.2% higher than paddy oilseed rape, respectively. The soil indigenous N and K supply in upland was 15.0% and 20.9% higher than that in paddy field, while the supply of P in upland was 39.2% lower than that in paddy field. The recovery efficiency of N and P in upland were higher than that of paddy field, while K recovery efficiency was lower than that of paddy field. In summary, the combined application of nutrients could improve rapeseed yield and nutrient use efficiency. The significant differences in rapeseed yield and nutrient utilization among different crop rotations were affected by nutrient types. Compared with the upland, to supplement the nutrients deficiency in the soil and achieve high-yield and high-efficiency production of rapeseed, rapeseed in paddy fields needs to pay more attention to the application of N and K fertilizers, while rapeseed in upland needs to be appropriately increased in P fertilizers compared with paddy fields.