Mastitis is a deleterious disease of dairy cattle, and its incidence is closely related with the innate immune response, including the complement system. Mannose-binding lectin-associated serine protease 2 (MASP2) is a functional central enzyme in the complement system. Here, we aimed to study single nucleotide polymorphisms (SNPs) of MASP2 and its relationship with mastitis and milk production in Chinese Holstein cattle. We found three novel SNPs, namely g.14047A > C, g.14248T > C and g.14391C > T, in MASP2. The SNP g.14047 A > C (GAA (Glu)>GAC (Asp)) at position 608aa of MASP2 was correlated with the CH50 level and the protein percentage. Meanwhile, the SNP g.14248 T > C (ATT (Ile) > ATC (Ile)) at position 675aa was also correlated with the CH50 value and the milk production. The haplotype combinations H2H2 and H2H4 showed a significant relationship with the CH50, SCS and the milk production abilities, respectively. Based on the SNPs identified in this gene, several genotypes and haplotypes, respectively, were found in Chinese Holstein cattle. The genotypes AC (g.14047 A > C) and TT (g.14248 T > C) and the haplotype combinations H2H2 and H2H4 may be used as molecular markers for breeding mastitis-resistant dairy cattle. The haplotype combination H1H2 should be gradually phased out in breeding programmes.