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For clarifying the genetic base of the variation of yield-related traits in soybean [ (L.) Merr.], we mapped quantitative trait loci (QTLs) for plant height and seed weight using a recombinant inbred line population derived from a cross between Chinese elite line Zhongpin03-5373 and cultivar Zhonghuang13. We detected 11 QTLs for plant height and 18 QTLs for seed weight across six diverse environments. These included three pairs of plant height- vs. seed weight-related QTLs located in close proximity to each other, with two pairs, vs. and vs. , sharing the same direction of additive effects. Individual QTLs explained 2.02 to 47.60% of the variation in plant height and 2.13 to 14.35% in seed weight. Two and five of the major QTLs discovered for plant height and seed weight, respectively, that were stable across environments in our study have been reported previously. Among them, four QTLs, , , , and , were not involved in digenic epistatic interaction in our biparental population, indicating that these QTLs will be useful for marker-assisted selection and should be targeted for the future identification of candidate genes. Moreover, eight QTLs for both plant height and seed weight were newly identified in our population.