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To systematically compare the immunogenicity differences between measles-mumps-rubella combined (MMR) vaccine and measles-rubella combined (MR) vaccine following first dose vaccination in 8–9-month-old infants, with emphasis on evaluating the response levels of measles, rubella and mumps-specific IgG antibody response levels induced by both vaccines, thereby providing evidence for optimized vaccine selection in China’s childhood immunization program. We conducted a randomized controlled trial enrolling 400 healthy infants aged 8–9 months from five counties and districts in Gansu Province, who were randomly allocated at a 1:1 ratio to either the MMR group (n = 200) or MR group (n = 200). Venous blood samples were collected from subjects before immunization and 4–8 weeks post-vaccination. Enzyme-linked immunosorbent assay (ELISA) was used to quantitatively detect measles-, rubella-, and mumps-specific (MMR group only) IgG antibody levels. Bayesian Generalized Linear Mixed Models (BGLIMM) were employed to analyze between-group differences in geometric mean concentrations (GMCs) of antibodies. Antibody data were fitted using Gamma distribution; fixed effects included age in months, gender, vaccine group (MMR vs. MR), sampling time point (pre- vs. post-immunization) and days post-vaccination while random effects included individual-level effects. Model evaluation metrics included Deviance Information Criterion (DIC) and effective number of parameters, with statistical inference based on 95% credible intervals (CrI) of the posterior distribution. Post-immunization, although the absolute measles IgG antibody GMC in the MR group (1338.36 IU/mL) was lower than that in the MMR group (1506.52 IU/mL), the MR group exhibited a substantially higher vaccine-induced fold-increase from baseline (248-fold vs. 200-fold). BGLIMM indicated that the increase in measles antibodies (GMC) was approximately 34% higher in the MR group compared to the MMR group (β = 0.29, 95% CrI: 0.08 to 0.49, corresponding to a GMC ratio of 1.34). No meaningful difference was observed in rubella IgG antibody GMCs between groups (31.78 vs. 26.67 IU/mL, fold-increase 29-fold vs. 22-fold, β = 0.01, 95% CrI: −0.13 to 0.16). Mumps IgG antibody GMCs in the MMR group was 164.37 U/mL (95% CrI: 145.13 to 186.16). Fixed-effects analysis revealed immunogenicity differences among the three antigens: measles (β = 5.12) > rubella (β = 3.26) > mumps (β = 2.61). Random-effects variance analysis demonstrated that inter-individual response heterogeneity exhibited substantial differences across antigens, with measles antibody showing the greatest inter-individual variability (precision for ID = 1.63, 95% CrI: 1.33–2.00), followed by rubella (precision = 3.56, 95% CrI: 2.83–4.43), and mumps showing the least (precision = 11.02, 95% CrI: 6.52–18.07). Both MMR and MR vaccines induce effective immune responses in 8–9-month-old infants; however, the MR vaccine demonstrates superior measles antibody responses compared to the MMR vaccine, consistent with established evidence that antibody responses tend to decrease as vaccine valency increases. These findings provide high-quality clinical evidence to inform vaccine selection and optimization in China’s childhood immunization program, suggesting that MR vaccine may be considered as an alternative for the first dose when maximizing measles antibody response is prioritized.