Abstract: In the context of agricultural enhancement, biochar serves as an effective soil amendment capable of enhancing soil fertility and augmenting 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, a field experiment with a split-plot design was conducted over a three-year period. This study entailed a comparative analysis of the impacts of various planting systems (monoculture of oil flax, monoculture of peas, and an intercropping system of oil flax and peas) alongside differing rates of biochar application (0, 10, and 20 t·hm⁻²) on the soil's fertility status and the yield and quality of the crops. The findings revealed that the application of biochar, in conjunction with intercropping practices, markedly improved the soil's nutrient content and the composite fertility index, with a notable increase ranging from 27.27% to 34.2% when compared to plots without biochar. Notably, the intercropping system with 20 t·hm⁻² of biochar exhibited the most pronounced enhancement. Application of 10 tons per hectare of biochar significantly bolstered soil fertility, crop yield, and quality across diverse planting configurations. Furthermore, this dosage of biochar substantially improved the crop yield, quality, and land equivalent ratio under various cropping systems. At the biochar application rate at10 t·hm⁻², compared with monoculture, the yields of flax and pea under intercropping increased by 33.95% and 11.29%, respectively. The increased application of biochar also elevated the oil content and the levels of unsaturated fatty acids (oleic acid, linoleic acid, and linolenic acid) while concurrently reducing the saturation of fatty acids (palmitic acid and stearic acid) in the oil flax grown in intercropping systems. Pathway analysis indicated that soil pH, alkali-hydrolyzed nitrogen, and available potassium exerted a predominantly indirect influence on crop yield, whereas soil organic matter, total nitrogen, and available phosphorus exerted a more direct influence. In conclusion, after three successive years of biochar application, soil fertility was significantly augmented under the 20 t·hm⁻² treatment, although crop yield was found to be diminished in comparison to the 10 t·hm⁻² treatment.