Salinity-alkalinity stress is one of the main factors limiting crop growth and production. However, few genetic sources that can be used to improve soybean salinity-alkalinity tolerance are available. The objective of this study was to determine the genetic mechanisms for salinity-alkalinity tolerance in soybean during germination by a genome-wide association study (GWAS) using 281 accessions with 58 112 single nucleotide polymorphisms (SNPs). Four salinity-alkalinity tolerance (ST) indices namely ST-GR (germination ratio), ST-RFW (root fresh weight), ST-DRW (root dry weight), and ST-RL (root length) were used to assess soybean salinity-alkalinity tolerance. A total of 8, 4, 6, and 4 quantitative trait loci (QTL) accounted for 3.83–8.01% phenotypic variation in ST-GR, ST-RL, ST-RFW, and ST-RDW, respectively. Two common QTL (qST.5.1 and qST.16.1) associated with at least three indices located on chromosome 5 (∼38.4 Mb) and chromosome 16 (∼29.8 Mb), were determined as important loci for controlling salinity-alkalinity tolerance in soybean. We also predicted candidate genes for the two QTL. The significant SNPs and common QTL as well as the salinity-alkalinity tolerant accessions will improve the efficiency of marker-assisted breeding and candidate gene discovery for soybean salinity-alkalinity tolerance.