This paper deals with the dynamical system that generalizes the MIC-Kepler system. It is shown that the Schrödinger equation for this generalized MIC-Kepler system can be separated in prolate spheroidal coordinates. The coefficients of the interbasis expansions between three bases (spherical, parabolic, and spheroidal) are studied in detail. It is found that the coefficients for this expansion of the parabolic basis in terms of the spherical basis, and vice versa, can be expressed through the Clebsch-Gordan coefficients for the group SU(2) analytically continued to real values of their arguments. The coefficients for the expansions of the prolate spheroidal basis in terms of the spherical and parabolic bases are proved to satisfy three-term recursion relations.