A novel, simple, cost-effective, reliable, and practical automatic column chromatography separation device capable of simultaneously purifying samples for radiogenic and non-traditional stable isotope analysis has been developed. The device avoids the use of any pump and features eluent driving by the siphon effect (gravity) and quantitative control by infrared droplet counting. Several factors affecting the control of droplets were investigated, including types and concentrations of eluents and the height of the liquid level. Results showed that accurate dripping of the eluent could be readily achieved by controlling the number of droplets under selected conditions. The separation performance of the device was first demonstrated by the elution of Sr and Cd in synthetic matrix solutions. The recoveries of Sr and Cd samples were better than 87.6 and 95.0%, respectively, and the whole procedure blank was about 0.3 ng for Sr and 0.1 ng for Cd. Finally, the reliability of the device was further validated by the purification of Sr and Cd from different geological reference materials (NIST 2711a, Nod-A-1, BCR-2, and BHVO-2). The determined Cd and Sr isotope values agree well with their reference values within the uncertainty range. All these results clearly demonstrate the reliability and practicability of the proposed device, which provides a promising method for the automated purification of isotope samples.