Fertilization and variety are the main factors limiting soybean yield in red soil area. To explore effects of the interaction between fertilization level and variety on soybean yield and plant nutrient accumulation, a dual factor completely randomized block design was adopted in this study, three fertilization levels were respectively set for the main treatment, no fertilization (CK), formula fertilizer 1 (L1), and formula fertilizer 2 (L2), and four soybean varieties were respectively set as vice treatment, Zhongdou 41 (ZD41), Nannong 99-6 (NN99), Nannong 57 (NN57), and Nannong 66 (NN66). Effects of 12 treatments on soybean grain and straw yield, yield increase rate, soil nutrients, and plant nutrient accumulation were analyzed. The results indicate that, there was significant increase in soybean grain and straw production under fertilization level and variety interaction (P<0.05), and the grain yield and straw yield of L2-NN66 were higher. Grain production capacity of nitrogen, phosphorus and potassium of soybean were affected under fertilization level and variety interaction. The main treatments of L1 and L2 were beneficial to increase soybean yield, and formula fertilizer L2 was better than L1 treatment. Content of soil available nitrogen, phosphorus and potassium increased significantly under fertilization level and variety interaction, and the increase of L2-NN66 was higher. The accumulations of nitrogen, phosphorus and potassium nutrients in soybean plants also increased under fertilization level and variety interaction, and L2-NN66 was also higher. From the correlation between soil nutrients at flowering stage and nutrient uptake of soybean plants at maturity stage, there is significantly positive correlation between the contents of soil alkaline hydrolyzed nitrogen, available phosphorus and potassium with the absorption of nitrogen, phosphorus and potassium nutrients of plants. Under the two-factor interaction of fertilization level and soybean variety, L2-NN66 was beneficial to soybean yield and plant nitrogen, phosphorus and potassium accumulation, which can be used as soybean fertilization level and variety combination to promote suitable planting.