Soybean (Glycine max L.), an important oilseed, food, and feed crop, has its yield and quality regulated by complex genetic networks. Shikimate O-hydroxycinnamoyltransferase (HCT) is a key enzyme in the phenylpropanoid metabolic pathway and plays important roles in plant secondary metabolism and growth and development. However, whether HCT is involved in regulating oil accumulation in soybean remains unclear. Here, we identified 39 GmHCT members in the soybean genome. Phylogenetic analysis classified these genes into three subgroups, revealing distinct variations in their conserved motifs and gene architectures. The analysis of cis-elements revealed that GmHCT promoters contain abundant motifs associated with hormonal regulation, abiotic stress, and developmental processes. The GmHCT members were widely distributed across 18 soybean chromosomes. Transcriptomic analysis indicated that the majority of GmHCT genes exhibited elevated expression levels during reproductive development, while specific members displayed particularly high expression in roots and nodules. By comparing materials with different quality phenotypes (high-protein high-oil (HPHO), high-protein low-oil (HPLO), low-protein high-oil (LPHO), and low-protein low-oil (LPLO)) and between wild and cultivated soybean (ZYD06 and SN14), six differentially expressed genes were screened, and four genes associated with oil accumulation were identified through haplotype analysis. Combining transcriptomic, RT-qPCR, and haplotype analyses, Glyma.04G040000 and Glyma.06G041400 were ultimately determined as key candidate genes linked to soybean oil accumulation. Further hairy-root transformation and gas chromatography analyses showed that upregulation of Glyma.04G040000 and Glyma.06G041400 increased fatty acid content in soybean hairy roots. Overall, this research presents a comprehensive genome-wide identification and characterization of the GmHCT gene family in soybean, and these identified candidate genes offer valuable references for the molecular breeding of oil-related and other quality traits in soybean.