Photic sneeze reflex (PSR) is an interesting but yet mysterious phenotype featured by individuals' response of sneezing in exposure to bright light. To uncover the underlying genetic markers (single nucleotide polymorphisms, SNPs), a genome-wide association study (GWAS) was conducted exclusively in a Chinese population of 3417 individuals (PSR prevalence at 25.6%), and reproducibly identified both a replicative rs10427255 on 2q22.3 and a novel locus of rs1032507 on 3p12.1 in various effect models (additive, as well as dominant and recessive). Minor alleles respectively contributed to increased or reduced risk for PSR with odds ratio (95% confidence interval) at 1.68 ([1.50, 1.88]) for rs10427255 and 0.65 ([0.58, 0.72]) for rs1032507. The two independent SNPs were intergenic, and collectively enhanced PSR classification by lifting the area-under-curve value in ROC curve to 0.657. Together with previous GWAS in other populations, the result substantiated the polygenic and non-ethnicity-specific nature behind the PSR phenotype.