The synthesized poly[N,N′-bis(3-silsesquioxanilpropyl)-thiocarbamide] (PSTM-3T) was used and the surface morphology and microstructure of it were analyzed by scanning electron microscopy with energy dispersive spectrometer (SEM/EDS). The molecular structure change of the PSTM-3T polymer of the PSTM-3T after treatment by acidic solution with different pHs was revealed using FT-IR experiments and ab initio calculations with density functional theory method. The sorption efficiency of the heavy metal ions depends on the molecular structure change of PSTM-3T after treatment of different pH aqueous solutions. After the treatment of acidic solution (pH = 2) of PSTM-3T, the polymer formed the tautomer state to increase the sorption efficiency for chromate ion. For the increment of pH value for acidic solution, the PSTM-3T polymer was dissociated to increase the sorption efficiency for copper ion.