Plant height and stem diameter are important agronomic traits in soybean, which have effect on yield and lodging. The objective of this study was to molecularly map the QTL conditioning plant height and stem diameter at different developmental stages of soybean growth. A population of 165 recombinant inbred lines (RILs) derived from a cross between Zhongdou 29 and Zhongdou 32 was used in this study. Based on unconditional and conditional QTL mapping methods, 18 QTLs for plant height and 19 QTLs for stem diameter were detected on eleven and nine linkage groups respectively. The number, additive effects and contribution rate of QTLs for plant height and stem diameter were different at different developmental stages, which indicated that these QTLs expressed timely and selectively. Three QTLs for plant height and one QTL for stem diameter were detected in three years, and six QTLs for plant height and two QTLs for stem diameter were detected in two years. The QTLs of plant height and stem diameter on linkage groups F were mapped to the same loci and they were expressed simultaneously from R1 to R4 stages. Compared with the late stages, more QTLs expressed in the early stages, and QTLs for plant height expressed more times than QTLs for stem diameter. The positive alleles of QTLs for plant height and stem diameter were from different parents. The developmental dynamic of QTLs for plant height and stem diameter was consistent with the correlation analysis of phenotypic traits at different developmental stages.