Cubic silicon carbide (3C-SiC) ceramics are one of the most promising candidates for structural materials in future fusion reactors. In a fusion environment, irradiation of high-energy neutrons induces a large number of point defects and many transmutants (H, He, Li, Be, B, Mg, Al and P). The interaction of irradiation-induced point defects with the transmutants affects the evolution of micro structure in 3C-SiC, however, the micro processes are still mysterious. In this work, we carry out systematical ab initio calculations concerning the interaction of irradiation-induced point defects with the transmutants in 3C-SiC. It is found that Li and Be atoms prefer to occupy the tetrahedral interstitial site surrounding by four carbon atoms. B atom is favorable to occupy the substitutional site of carbon, while Mg, Al, and P atoms prefer to occupy the substitutional site of silicon. Moreover, only B, Mg and Al pairs have positive binding energies, which suggests that B, Mg, and Al pairs tend to segregate and form clusters at substitutional sites. Vacancy and self-interstitial atom can act as trapping centers for transmutants, especially for Mg. The electron density and the volume difference are analyzed to understand the underlying reasons controlling the interaction of point defects with transmutants.