Heavy metal ions in water, cosmetics, and arable land have become a world-wide issue as they cause a variety of diseases and even death to humans and animals when a certain level is exceeded. Therefore, it is necessary to development a new kind of sensor material for the determination of heavy metal ions. In this paper, we present an electrochemical sensor based on composite material (thiol(–SH) grafted poly(3,4-proplenedioxythiophene) (PProDOT(MeSH)2)/ porous silicon spheres (Si) composite, denoted as PProDOT(MeSH)2@Si) from the incorporation of thiol(–SH) grafted poly(3,4-proplenedioxythiophene) (PProDOT(MeSH)2) with porous silicon spheres (Si) for the electrochemical detection of heavy metal ions (Cd(II), Pb(II), and Hg(II)). The PProDOT(MeSH)2@Si composite was synthesized via a chemical oxidative polymerization method. The structure and morphology of PProDOT(MeSH)2@Si composite were characterized by Fourier transform infrared (FT-IR), Ultraviolet–visible spectroscopy (UV–Vis), X-ray diffraction (XRD), scanning electron microscope (SEM), Transmission electron microscope (TEM), and Brunauer−Emmett−Teller (BET). Furthermore, the electrochemical performance of PProDOT(MeSH)2@Si was evaluated by detecting of Cd(II), Pb(II), and Hg(II) ions using the differential pulse voltammetry (DPV) method. The relationship between structural properties and the electrochemical performance was systematically studied. The results showed that the entry of two thiol-based chains to the monomer unit resulted in an increase in electrochemical sensitivity in PProDOT(MeSH)2, which was related to the interaction between thiol group(-SH) and heavy metal ions. And, the combination of PProDOT(MeSH)2 with Si could improve the electrocatalytic efficiency of the electrode material. The PProDOT(MeSH)2@Si/GCE exhibited high selectivity and sensitivity in the rage of 0.04 to 2.8, 0.024 to 2.8, and 0.16 to 3.2 μM with the detection limit of 0.00575, 0.0027, and 0.0017 µM toward Cd(II), Pb(II), and Hg(II), respectively. The interference studies demonstrated that the PProDOT(MeSH)2@Si/GCE possessed a low mutual interference and high selectivity for simultaneous detection of Cd(II), Pb(II), and Hg(II) ions.