A systematic investigation on all possible substituted fullerene isomers of C38B2, C38N2 and C38BN has been performed using the semiempirical methods AM1 and MNDO. The heat of formation, stabilization energy, HOMO–LUMO gap, the strain, the absolute hardness and electronegativity have been studied. The calculations show that the order of stability is C40 > C38B2 > C38BN > C38N2, which is similar to heterofullerenes C36 though somewhat different from the hetero-C60 cluster. The strain in C38XY rises relative to the C40 cluster according to POAV analysis, and the absolute hardness and the electronegativity of C40 is larger from an application of the HSAB principle. The selectivity of the substitution positions is commonly determined by the conjugative effect and tension. The vibration spectra for the doped fullerenes have been calculated, which could serve as a framework to interpret future experimental results.