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This study was conducted with two soybean cultivars, Liaodou 13 (L13, phosphorus (P)-efficient) and Tiefeng 3 (T3, P-inefficient), to investigate the effects of biochar on soybean yield and photosynthetic physiological parameters, at four biochar application rates (0, 1, 5, and 10%, w/w), and two fertilization treatments (0 and 150 kg ha−1). Grain yield, plant biomass, P accumulation, leaf net photosynthetic rate (Pn), chlorophyll index (Chl), nitrogen balance index (NBI), sucrose phosphate synthase (SPS), and sucrose synthase (SS) activities, soluble sugar, sucrose and starch contents, and leaf area duration (LAD) were measured. Biochar had positive effects on Pn, Chl, NBI, SPS, and SS activities, and leaf soluble sugar, sucrose, and starch contents of both genotypes, these effects increased with biochar application rate. L13 benefited more efficiently from biochar than T3 did, as the grain yield of L13 significantly increased by 31.0 and 51.0%, at 5 and 10% biochar, respectively, while that of T3 increased by 40.4 at 10% biochar application rate, as compared with controls. The combined application of biochar and fertilizer boosted the positive effects described, but no difference was found for grain yield in L13 among biochar application rates, while grain yield of T3 continually increased with biochar rate, among which, 1% biochar combined with 150 kg ha−1 fertilizer resulted in T3 yield increment of more than 23%, compared with the application of 150 kg ha−1 fertilizer alone. Altogether, our results indicated that the application of biochar enhanced carbon assimilation in soybean, resulting in increased biomass accumulation and yield. Differences in genotypic responses to biochar highlight the need to consider specific cultivars and biochar rate, when evaluating the potential responses of crops to biochar.