Abstract The bismuth-, antimony- and arsenic-containing complexes are known as antibacterial and antitumor drugs in the field of clinical medicine. It is of great physiological significance to understand the structures of these complexes with thiolate ligands. But the optimal theoretical calculation method for these metal thiolate complexes is not certain. In this work, the molecular structures, vibrational spectra and absorption spectra of metal thiolate complexes M(SC6H5)3 (M=Bi, Sb or As) have been calculated with density functional (mPW1PW, B3LYP, TPSSh and OLYP). The theoretical results were compared to the available experimental data. It is demonstrated that mPW1PW functional is superior to other functionals (B3LYP, TPSSh and OLYP) in predicting molecular structures and vibrational spectra of Sb-thiolate and As-thiolate complexes. For Bi-thiolates complex, the hybrid density functional B3LYP gives better performance than other methods. The theoretical absorption spectrum of Bi(SC6H5)3 from B3LYP functional is similar to the available experimental data, which confirms the rationality of theoretical calculation method. Furthermore, the theoretical method was successfully used to predict the formation process of the Bi–O bond in Bi7-metallothionein, an important product in vivo on effectively reducing side effect of metal-containing drugs. The confirmed calculation method for each complex will be helpful for our further understanding on the complexation structure of the Bi-, Sb- and As-containing complexes with thiolate ligands.