Water-soluble protein concentration (WSPC) of soybean (Glycine max (L.) Merrill) is an important factor affecting the quality of soybean-derived food and the aesthetic appearance of soybean products. In the present study, a representative soybean population of 178 elite accessions was used to determine quantitative trait nucleotides of WSPC via a genome-wide association study (GWAS). In total, 33 149 single-nucleotide polymorphisms (SNPs) with minor allele frequencies ≥5% and missing data ≤10% were applied in assessing the level of linkage disequilibrium. Finally, three association signals were identified related with WSPC through GWAS, including one novel locus and two known loci that overlapped the genomic region of reported quantitative trait loci. Thirty candidate genes located in the 200-kb genomic region of each peak SNP were detected and mainly grouped into the classes of protein synthesis/modification/degradation, RNA regulation of transcription, amino acid synthesis/metabolism, transport, hormone metabolism, signalling, development, lipid metabolism, and secondary metabolism. Through a gene-based association, 21 SNPs from eight genes were detected. Among them, four genes have been recognised as significant factors in mediating WSPC. The loci identified with beneficial alleles and candidate genes may be of great value for further functional analysis and marker-assisted selection of WSPC in soybean.