Three different methods (a sulfuric acid method, sodium chloride method and vibration method) were used to extract extracellular polymeric substances (EPS) from Cupriavidus pauculus 1490 (C. pauculus 1490) in the present study. The sodium chloride method was able to extract the maximum amount of EPS (86.15 ± 1.50 mg g−1-DW), and could ensure minimum cell lysis by detecting glucose-6-phosphate dehydrogenase activity and using scanning electron microscopy. This method was therefore selected as the optimal extraction method and used in subsequent experiments. On this basis, the tolerance of C. pauculus 1490 and variations in EPS secretion after the addition of different metal ions was investigated. The tolerance levels of C. pauculus 1490 to Cd(II), Ni(II), Cu(II) and Co(II) were 300 mg L−1, 400 mg L−1, 400 mg L−1 and 400 mg L−1, respectively. Low concentrations of these heavy metal ions could promote bacterial growth, while increased concentrations were found to inhibit it. The results show that metal ions, especially Cd(II), stimulate the secretion of EPS, with an EPS yield reaching 956.12 ± 10.59 mg g−1-DW at 100 mg L−1. Real-time polymerase chain reaction (PCR) analysis showed that the key EPS synthetic genes, epsB, epsP and Wzz, were up-regulated. Fourier transform infrared spectroscopy analysis suggested that abundant functional groups in EPS play an important role in heavy metal ion complexation. These results will contribute to our understanding of the tolerance mechanism of microorganisms in the presence of different types and concentrations of metal ions.