Plant height is a key agronomic trait in soybean (Glycine max L.), as it directly influences the number of nodes on the main stem, pod number per plant, yield, and lodging resistance. Identifying genes that regulate plant height is therefore essential for optimizing plant architecture and enhancing soybean productivity. Through a genome-wide association study (GWAS), we identified qGPH3 as a region associated with soybean plant height that co-located with qBPH16, a quantitative trait locus (QTL) derived from a bulked segregant analysis by sequencing (BSA-seq) and mapping to chromosome 17. RT-qPCR analysis revealed that Glyma.17 g082100 expression levels are significantly higher in the dwarf parent Wandou 15 than in the tall parent Xudou 18 used for the QTL mapping. We detected four haplotypes for this gene, with soybean accessions carrying Glyma.17g082100^Hap3 being the shortest, whereas those with Glyma.17g082100^Hap4 were the tallest. Functional validation using gene editing and overexpression in transgenic lines confirmed Glyma.17 g082100 as the causal gene regulating soybean height underlying qGPH3 and qBPH6. This bHLH transcription factor gene, designated GmBIM1, is highly expressed in developing stems and leaf buds and encodes a nucleus-localized protein. Our findings identify useful genetic resources for improving soybean yield potential through targeted breeding of plant architecture.