In this work, the application of stir bar sorptive extraction (SBSE), as a fast and conventional method, has been investigated for the simultaneous preconcentration and determination of trace amounts of Cd(II) and Cu(II) ions in natural samples. For this purpose, the surface of stir bar was functionalized by amine functionalized nanoporous silica and characterized by IR spectroscopy, X-ray powder diffraction (XRD), Atomic force microscopy (AFM) and N2 adsorption. In this approach, after the preconcentration of Cd(II) and Cu(II) ions and removing the matrix interferences using modified stir bar, the amounts of these ions were determined in eluent by flame atomic absorption spectroscopy (FAAS). Various parameters on adsorption and elution steps including pH of sample, adsorption kinetic, eluent parameters (type, volume and concentration) and elution time, have been optimized in this study. The limits of detection (LOD) were 1.6 and 13.8 ng mL-1 (recovery of 83.5 and 88.1%) for cadmium and copper ions, respectively. The preconcentration factors were 133 and 137 and the relative standard deviations (RSD) of the method were 5.7 and 4.6% for Cd(II) and Cu(II) ions, respectively. As the key point in this study seems to be stir bar nanoporous structure, the analytical performance of this stir bar was compared to non-porous ones. The accuracy of this novel method has been confirmed using some standard references materials. Finally the potential of this method was investigated by determination of Cd(II) and Cu(II) ions in some real samples with complicated matrixes.