Abstract: In the context of agricultural enhancement, biochar serves as an effective soil amendment, with the capacity to enhance soil fertility and augment crop yield. To ascertain the efficacy and value of biochar in the cultivation of oil flax within the cool, arid farming region of Gansu Province, we conducted a 3-year field experiment with a split-plot design. The study entailed a comparative analysis of the effects of different cropping patterns (monocropping of oil flax, monocropping of pea, and intercropping of oil flax and pea), along with the different application rates of biochar (0, 10, and 20 t·hm⁻²), on the soil fertility status, and yield and quality of the crops. The findings revealed that compared with no biochar application, the application of biochar enhanced the soil nutrient contents and soil integrated fertility index. The intercropping pattern with 20 t·hm⁻² of biochar was characterized by the most pronounced enhancement. Biochar application increased crop yield and yield components of different cropping configurations. Compared with no biochar application, the yields of oil flax and pea with biochar application under monocropping pattern increased by 5.85%–7.25% and 12.04%–16.86%, respectively, and the yields of oil flax and pea with biochar application under intercropping pattern increased by 9.64%–19.79% and 14.47%–19.78%, respectively. Furthermore, land equivalent ratio of intercropping pattern were higher than 1, land use efficiency increased, and intercropping pattern offered significant advantages. With respect to oil flax, application of biochar also contributed to elevations in oil contents and the levels of unsaturated fatty acids (oleic acid, linoleic acid, and flax acid), whilst concurrently contributing to reductions in the contents of saturated fatty acids (palmitic acid and stearic acid) in intercropped oil flax. Furthermore, pathway analysis indicated that soil pH, alkali-hydrolyzed nitrogen, and available potassium had a predominantly indirect influence on crop yield, whereas soil organic matter, total nitrogen, and available phosphorus had more direct effects. In conclusion, after three successive years of biochar application, there was a significant augmentation of soil fertility in plots receiving the 20 t·hm⁻² of biochar, although crop yield was found to be diminished compared with that in soil amended with 10 t·hm⁻² biochar. Therefore, continuous biochar application over several years can improve soil fertility, but excessive accumulation of biochar can reduce crop yield and quality.