Seed purity is one of the core indicators of seed quality. Molecular markers have a good application prospect in seed purity identification because they are not limited by environment and season, and have a good discrimination ability. In this study, a combination of eight pairs of primer was selected from the industry standards suitable for purity assessment which had high heterozygosity and variety discrimination ability could identify more than 90% of approved varieties, and 96% of approved varieties have more than four heterozygous loci. SSRs and plant inspection were used to compare their ability to assess seed purity, 38 maize samples collected from national seed market were both tested by field planting and SSR purity. An average rate of 0.6% of inbred seedlings and 1.8% of off-types was detected by 8 SSR markers combination, and compared with the average rate of 1.4% for inbred seedlings and 0.6% for off-types in field planting identification. The purity values detected by the two methods had good correlation. The result of field inspection was consistent with SSR for identifying off-types and typical individuals, and SSR could accurately distinguish weak seedlings and diseased plants that were difficult to identify in the field. Significant separation of genotypes and phenotypes were observed in 7 samples with grade 3-5 of uniformity detected by SSR markers. Atypical seedlings caused by poor uniformity are difficult to identify in variety purity assessment both for SSR and field inspection.