5-Benzylidene-2-thiobarbituric acid (BzTBA), a pyrimidine derivative, was used to modify the surface of silica gel–chloropropyltrimethoxysilane (Si-Cl) via chemical immobilization to produce a new pyrimidine silica phase (Si-BzTBA). Identification of the surface modification was characterized and performed on the basis of infrared as well as elemental analysis. Thermal desorption method was found to give 0.129–0.143 mmol g −1 as surface coverage values. Metal sorption properties of Si-BzTBA were also studied and the evaluated results refer to the high metal sorption of Si-BzTBA for copper(II), mercury(II), cadmium(II), and lead(II) with the same order. These four Si-BzTBA–metal complexes were also synthesized and the stoichiometric ratios were identified as 1:1 except lead complex was found to give a 1:2 ratio. Electron impact–mass spectrometric analysis (EI-MS) with 70 eV ionization energy was used as a potential thermal method for the confirmation of surface modification of Si-BzTBA and its metal complexes based on fragmentation elucidation of thermally desorbed ion peaks. The EI-MS of Si-BzTBA was found to show several characteristic fragment ion peaks that are directly related to the chemical binding of BzTBA to SiCl phase. Differential scanning calorimetry study (DSC) was also performed to evaluate the various kinetic and thermodynamic parameters of thermal degradation processes and have been enumerated. The results of EI-MS and DSC are very similar in many respects.