Objective: To assess the association of JAG2 gene single nucleotide polymorphisms with the occurrence of nonsyndromic cleft lip with or without cleft palate (NSCLP) among northwest Chinese population. Methods: A case-control study was carried out on 301 NSCLP patients and 304 healthy controls. An iMLDR™ genotyping technique was used to detect three single nucleotide polymorphisms (SNPs) [rs741859 (T/C), rs11621316 (A/G) and rs1057744(C/T)] of the JAG2 gene. Allelic and genotypic frequencies and haplotypic distribution among the two groups were compared. Results: A significant difference was found in the frequency of C and T alleles for rs741859 between the two groups. The CT genotype of rs741859 could significantly reduce the risk for NSCLP to 65% (P < 0.05) and the risk for cleft lip with or without cleft palate (CL/P) to 62% (P < 0.05). rs11621316 and rs1057744 are in the same linkage disequilibrium (LD) region with a high degree of linkage (r² > 0.8), whose distribution difference between the two groups was not statistically significant (P > 0.05). Conclusion The CT genotype of the JAG2 gene rs741859 may confer a protective effect for NSCLP among northwest Chinese population.