The pair correlation energy of bonding electrons is used and analyzed in the cal- culation of C-H and C-Y (Y = F, O, N) bonding electron pairs in CH3X (X = F, OH, NH2) isoelec- tronic systems based on intra- and interpair correlation energy results at both MP2-OPT2/6- 311++G(d) and MP2-OPT2/cc-pVtz levels with MELD program. Comparison of two set results shows that cc-pVtz and 6-311++G(d) give more correlation energy of valence electrons and innermost core electron pairs, respectively in these systems, resulting that the total correlation energy with cc-pVtz basis of each system is larger than that with 6-311++G(d). Investigations of pair correlation energy show that with the decrease of electronegativity of X atom and the increase of H atoms in these CH3X (X = F, OH, NH2) systems, the pair correlation energy of 1sC2 of the C atoms is transferable, and the correlation energy of C-H bonding electron pair with little changes is of approximate transferability, while those of C-Y (C-F, C-O, C-N) bonding electron pair decrease in a large extent from CH3F through CH3OH to CH3NH2 molecules. It is suggested that the study of pair correlation energy of bonding electrons will further deepen the understanding of electron corre- lation effect from traditional chemical bonding concept.