In this experiment, eight different genotype soybean varieties were used and five fertilization gradients were set in two different ecological regions, Gongzhuling and Dunhua. The purpose is to study response of different genotype soybean to fertilizer, explore influence of different fertilizer on yield and agronomic traits of different genotypes of soybean in two ecological regions. The results showed that the yield of different genotype soybean varieties increased with the fertilizer levels, then gradually decreased. Yield of‘Jiyu 86’,‘Jidadou No.3’,‘Jinong 38’and‘Jiyu 301’was higher under different fertilization. There was a significant difference in the response of yield of different varieties to fertilization,‘Jiyu 86’and‘Jiyu 47’were more sensitive to fertilizer, their yield were highest when the fertilizer was 210 and 180 kg per hectare, respectively, which were 25.5 and 11.9 percent higher compared to non-fertilization. Response of yield of‘Jidadou No.3’and‘Jinong 38’to fertilizer was not sensitive. Their yield were highest when the fertilizer was 157.5 and 135 kg per hectare, respectively, which were 12.28 and 7.57 percent higher compared to non-fertilization. Fertilization significantly promoted the plant height. There was a tendency to increase the number of nodes with the increase of fertilization. Pod weight, grain weight and hundred-grain weight increased with the fertilizer levels, then gradually decreased. Therefore, amount of fertilizer should be adjusted based on soybean varieties response to fertilizer to achieve maximum benefit in the production.