Haplotype-based breeding involving multi-marker association analysis is a promising approach to developing custom-designed high-yielding crop varieties. Here, we reported multi-marker association analysis for the number of pods per plant (PNP), the number of seeds per plant (SNP), 100-seed weight (HSW), and seed yield per plant (SYP) using 211 cultivated soybean accessions. The field experiment was conducted across six environments following a randomized complete block design with three replications. Genome-wide association study (GWAS) using 12,617 single-nucleotide polymorphism (SNP) markers from NJAU 355K SoySNP Array identified 57 significant marker associations with the studied traits across the six environments. Out of these, six markers that were consistently associated with the yield traits in two or more environments were considered stable and selected as the reference markers for building haplotype block/loci. The multi-marker association analysis within the haplotype-based framework revealed various allelic combinations regulating the phenotypic variations for the studied yield-related traits in soybean. These haplotype alleles may serve as genomic resources in breeding programmes aimed at improving the yield potential of soybean.