The pair correlation energy of bonding electrons is used and analyzed in the calculation of C-H and C-Y (Y = F, O, N) bonding electron pairs in CH3X (X = F, OH, NH2) isoelectronic systems based on intra- and interpair correlation energy results at both MP2-OPT2/6311++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 1s(C)(2) 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 correlation effect from traditional chemical bonding concept.