Reduction of soil fertility and production efficiency resulting from excessive application of chemical fertilizers is universal in rapeseed-growing fields. The main objective of our study was to assess the effects of biochar combined with nitrogen fertilizer reduction on soil aggregate stability and rapeseed yield and to identify the relationship between yield and soil aggregate stability. A two-factor field experiment (2017–2019) was conducted with biochar (0 (C0), 10 (C10), 20 (C20) and 40 t·ha−1 (C40)) and nitrogen fertilizer (180 (N100), 144 (N80) and 108 kg N·ha−1 (N60)). Experimental results indicated that under N100 and N80 treatments, C10 significantly increased the macro-aggregates (R0.25), mean weight diameter (MWD) and geometric mean diameter (GMD) of soil water stable aggregate by 14.28%–15.85%, 14.88%–17.08% and 36.26%–42.22%, respectively, compared with C0. Besides, the overall difference of the soil water-stable aggregate content in 2–5 mm size range among nitrogen treatments was significant under the application of C10, which increased by 17.04%–33.04% compared with C0. Total organic carbon (TOC) in R0.25 of soil mechanical-stable aggregates was basically all increased after biochar application, especially in 0.25–1 mm and 1–2 mm aggregates, and had an increasing trend with biochar increase. C10 significantly increased rapeseed yield by 22.08%–45.65% in 2019, compared with C0. However, the reduction of nitrogen fertilizer reduced the two-year average rapeseed yield, which decreased by 11.67%–31.67% compared with N100. The highest yield of rapeseed was obtained by N100C10 in two consecutive years, which had no statistical difference with N80C10. However, the two-year yields of N80C10 were all higher than those of N100C0 with increase rate of 16.11%, and which would reduce 35.43% nitrogen fertilizer in the case of small yield difference, compared with the highest yield (2.67 t·ha−1) calculated by multi-dimensional nonlinear regression models. The regression analysis indicated R0.25, MWD and GMD had the strong positive associations with rapeseed yield, whereas percentage of aggregate destruction (PAD0.25) had a significant negative correlation with rapeseed yield. This study suggests that the application of biochar into upland purple soil could improve soil structure, increase the content of TOC in macro-aggregates under nitrogen fertilizer reduction as well as replace part of nitrogen fertilizer to achieve relatively high rapeseed yield.