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Although crop rotations have been widely shown as an effective approach for improving yield or soil quality in the long term, the relationship between crop rotations and quality traits of crop or biochar-based fertilization is still unclear. To address this, we conducted a long-term field experiment in the Heilongjiang province of China to investigate the effects of crop rotation and biochar-based fertilizer application on the crop yield, soil parameters, crop quality, and agronomic traits in 2014–2020. The effects of rotations on crop production and soil properties were evaluated with the average yield variability during the 7 years of this study. Our results showed that the diversified corn and soybean rotations had a significant positive effect on average crop yield compared with their monocultures. The corn yield was enhanced by 0.6 Mg ha−1 (5.4%) in the corn–soybean–corn (CSC) crop sequence compared with monoculture corn. Similarly, soybean yield was enhanced by 0.21 Mg ha−1 (9.7%) in the soybean–corn–corn (SCC) crop sequence compared with monoculture soybean. However, a negative effect of crop rotations was detected on the protein content of soybean compared with the monoculture soybean, while a positive effect was detected on oil content. Additionally, no differences were detected in crop yield between biochar-based fertilization and mineral fertilization treatments, but a significant positive effect of biochar-based fertilization was observed for any crop on both protein and oil content. A significant effect of crop rotation was found on the percentage of total soil N (TN), available soil N (AN), and available soil K (AK) content. The SSS crop sequence treatment illustrated the highest TN values at 0.18%. The CCC crop sequence treatment increased AN and AK content by 9.1% and 7.8%, respectively, compared with SSS (p < 0.05). We conclude that crop rotations increase crop yield and biochar-based fertilizer application, improving crop quality traits in the long term. Thus, the addition of biochar-based fertilizer could efficiently enhance the yield and quality of crop in the rotation cropping system. The findings of this study may provide useful information for designing sustainable cropping systems based on rotations. [ABSTRACT FROM AUTHOR]