Background: Large-scale single nucleotide variation (SNV)-based blood group genotyping assays have been made available for over a decade. Due to differences in ethnic groups, there is much diversity in clinically important blood group antigens and genetic variants. Here, we developed a robust matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based blood group genotyping method on MassARRAY system. Study Design and Methods: A total of 1428 donors were enrolled into three groups: (a) reagent red cell donors; (b) rare donor or common antigen-negative donors; and (c) group O, R1R1/R2R2 donors. Forty-two SNVs were designed for determining nine blood groups, with X/Y chromosome in two multiplex reactions, on MassARRAY 96-well format system. Further targeted sequence analyses were performed by Sanger sequencing. Results: WHO reference reagent (NIBSC code: 11/214) was tested for concordance with the provided genotype results. Among the donors, concordance rate was over 99%. Alleles of important phenotypes such as Mi(a+), Di(a+), and Asian-type DEL and alleles of rare blood groups such as Fy(a−), Jk(a−b−) and s− were screened. Three types of discrepancies were found. Serologically, the ‘N’ antigen was expressed on genetically MM with GYP*Mur red blood cells and caused genuine discrepancies (9.5%). Genetically, allele dropout (ADO) was caused by rare SNV in the primer for Ss genotype (2.1%) and partial insertion of RHD genes (0.9%) led to difficulties in predicting phenotypes. Conclusion: Hemo panel module and MassARRAY System in 96-well format showed good performance in terms of large-scale blood group genotyping and phenotype predictions. Implementation of this method is effective for routine blood group genotype screening of donors.