Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects.  Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height.  Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping.  This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP).  The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers.  Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome.  Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18).  Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance.  They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively.  Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.