We used 135 genome-wide simple sequence repeat (SSR) markers to assess genetic diversity, population structure and linkage disequilibrium (LD) of 196 soybean landraces. On the basis of estimated population structure, we conducted association mapping for soybean resistance to common cutworm (CCW) using genomic-wide mapping strategies and detected the elite alleles of soybean resistance to CCW, along with their carriers. In addition to wide geographic origin, the population showed extensive genetic variation, and 17.9% of the SSR pairs were in LD (with D'>0, P<0.05). The extent of LD was > 6.61 cM with genetic distance of locus pairs for the loci in the same linkage group (LG). Association analysis revealed 7 SSRs associated with soybean resistance to CCW (P<0.01): 4 accounted for >10% of the total genetic variation for resistance; 6 located in the linkage groups reported to be related to soybean resistance to insects. Allele effect analysis revealed that the alleles related to larval weight of CCW mainly had a negative effect, the allele Sat_334-A208 showing the largest negative effect (43.9%). The alleles related to leaf consumption of single larva (LCL) and pupal weight (PW) of CCW mainly had a positive effect, the allele Satt199-A186 showing the largest positive effect for LCL (36.4%) and the allele Sat_320-A286, the largest positive effect for PW (31.4%).