In a 2-year experiment, we detected QTL for yield per plot and agronomic trait content by using the recombination inbred lines (RIL) population derived from a cross between Jindou 23 soybean as the female parent and semi-wild soybean parent (ZDD2315) 447. In all, 12 QTL with additive effects for yield per plot, grain weight per plant, stem weight per plant, grain weight/stem weight, branch number, nodes of the main stem, plant height, and pod height were mapped in the linkage groups A1, A2, H_1, I, J_2 and M. The 5 traits of yield per plot, plant height, grain weight per plant, branch number and nodes of the main stem were the positive effects donated by Jindou 23. We detected 11 QTL pairs with epistatic effects for pod height, plant height, grain weight per plant and stem weight per plant in the RIL, We found an interaction with the environment for 22 QTL. The epistatic effects and the environmental played an important role in the inheritance of yield per plot and agronomic traits in soybean. In terms of molecular marker-assisted breeding, in considering that QTL play a major role at the same time, epistatic QTL is conducive to the stable expression and genetic of traits.