Abstract: The objective of this study was to investigate the effect of biochar-based fertilizer with different formulations on crop yield, grain quality and nutrients use efficiency, which could provide a scientific basis for biochar-based fertilizer development in agriculture. Field experiment was conducted in Luhe district, Nanjing City, Jiangsu province. There were five treatments in total including no any fertilizer (NoF), applying chemical compound fertilizer as base fertilizer (CF), and applying 3 biochar-based chemical fertilizers with different formulations instead of chemical compound fertilizer (abbreviated as BF1, BF2 and BF3). Crop yield, grain quality, nutrients use efficiency and soil nutrients content by crop harvest were analyzed. Compared to CF, BF2 had no effect on rice grain yield, whereas they increased the yield of winter-wheat significantly. The wheat yield under BF2 treatment increased by 20.39% compared with CF. The rice yields under BF2 and BF3 treatments were significantly higher than those under BF1 treatment, increasing by 22.61% and 19.38% respectively. During the entire crop rotation cycle, the total output of rice and wheat was the highest under the BF2 treatment, increasing by 8.58%, 14.76% and 7.67% respectively compared with the CF, BF1 and BF3 treatments. Compared to the CF treatment, the BF1 treatment significantly reduced the chalkiness of rice by 1.58 percentage points. The chalkiness of rice with the BF1 treatment was also significantly lower than the BF2 and BF3 treatment. The protein content of rice grains under BF2 treatment was 1.69 percentage points higher than the BF1 treatment. Compared to the CF treatment, protein content, wet wheat gluten percentage and hardness of wheat grains under the BF2 treatment increased by 1.90, 4.46 and 7.73 percentages respectively, and the sedimentation index of wheat under the BF2 treatment was significantly higher than that under the BF1 treatment. Compared to CF, BF2 treatment enhanced the fertilizer use efficiency during the rice and wheat seasons. During the rice season, the fertilizer contribution rate, the agronomic efficiency of fertilizers and the partial factor productivity of fertilizers increased; during the wheat season, they also increased. Moreover, the fertilizer use efficiency under the BF2 treatment was higher than that of the other two biochar-based fertilizer treatments. The responses of crop yield and grain quality to biochar-based compound fertilizer depends on crop type. In the short term, applying biochar-based compound fertilizer instead of chemical compound fertilizer could increase grain yield and fertilizer use efficiency of wheat and improve the appearance quality of polished rice. Elevating the ratio of K:P in biochar-based compound fertilizer could boost the agronomic effect of biochar-based fertilizer if the total amount of P and K were constant.