This study was conducted to estimate the genetic parameters and breeding values for birth weight (BW) and reproductive and milk traits of the Egyptian buffalo. Moreover, the relationship among the estimated breeding values was analyzed using the principal component analysis, and selection index was constructed to improve performance. A total of 65,734 records of 2426 buffalo cows calved from 1980 to 2018 were collected from five buffalo experimental herds to estimate the genetic parameters and breeding values and then standardized for use in the principal component analysis with covariance matrix. The estimated heritability values were low for BW, total milk yield (TMY), gestation length (GL), days open (DO), calving interval (CI), calving ease (CE), and age at first calving (AFC), but they were moderate for lactation period (LP). The repeatability estimates were very low for DO and CI but were low for BW, GL, and CE, whereas they were moderate for TMY and LP. Of eight principal components (PCs), four PCs had > 1 eigenvalues, and the total variance explained was 70.37%. The variances explained for PC1, PC2, PC3, and PC4 were 25.71%, 18.20%, 13.28%, and 13.18%, respectively. The standardized estimated breeding values of CI and DO, TMY and LP, GL and CE, and BW and AFC correlated with PC1 (0.915 and 0.925), PC2 (0.760 and 0.758), PC3 (− 0.622 and 0.567), and PC4 (0.710 and 0.438), respectively. These results suggest that BWand reproduction traits would respond slowly to selection, whereas production traits would respond faster, and the uses of PCs depend primarily on the selection purpose that could be used in the genetic improvement programs of the Egyptian buffalo instead of the traditional selection index.