The proper and efficient utilization ofnatural genetic diversity can significantly impact cropimprovements. Plant height is a quantitative trait governingthe plant type as well as the yield and quality ofsoybean. Here, we used a combined approach includinga genome-wide association study (GWAS) andhaplotype and candidate gene analyses to explore thegenetic basis of plant height in diverse natural soybeanpopulations. For the GWAS analysis, we used thewhole-genome resequencing data of 196 diverse soybeancultivars collected from different accumulatedtemperature zones of north-eastern China to detect thesignificant single-nucleotide polymorphisms (SNPs)associated with plant height across three environments(E1, E2, and E3). A total of 33 SNPs distributed onfour chromosomes, viz., Chr.02, Chr.04, Chr.06, andChr.19, were identified to be significantly associatedwith plant height across the three environments.Among them, 23 were consistently detected in two ormore environments and the remaining 10 were identifiedin only one environment. Interestingly, all the significantSNPs detected on the respective chromosomesfell within the physical interval of linkage disequilibrium(LD) decay (± 38.9 kb). Hence, these genomicregions were considered to be four quantitative traitloci (QTLs), viz., qPH2, qPH4, qPH6, and qPH19,regulating plant height. Moreover, the genomic regionflanking all significant SNPs on four chromosomesexhibited strong LD. These significant SNPs thusformed four haplotype blocks, viz., Hap-2, Hap-4,Hap-6, and Hap-19. The number of haplotype allelesunderlying each block varied from four to six, andthese alleles regulate the different phenotypes of plantheight ranging from dwarf to extra-tall heights. Ninecandidate genes were identified within the four haplotypeblocks, and these genes were considered putativecandidates regulating soybean plant height. Hence,these stable QTLs, superior haplotypes, and candidategenes (after proper validation) can be deployed for thedevelopment of soybean cultivars with desirable plantheights.