A new two-stage chemical separation method was established using an anion exchange resin, Eichrom 1 × 8, to separate Mo and W from four natural rock samples. First, the distribution coefficients of nine elements (Ti, Fe, Zn, Zr, Nb, Mo, Hf, Ta, and W) under various chemical conditions were determined using HCl, HNO3, and HF. On the basis of the obtained distribution coefficients, a new technique for the two-stage chemical separation of Mo and W, along with the group separation of Ti-Zr-Hf, was developed as follows: 0.4 M HCl-0.5 M HF (major elements), 9 M HCl-0.05 M HF (Ti-Zr-Hf), 9 M HCl-1 M HF (W), and 6 M HNO3-3 M HF (Mo). After the chemical procedure, Nb remaining in the W fraction was separated using 9 M HCl-3 M HF. On the other hand, Nb and Zn remaining in the Mo fraction were removed using 2 M HF and 6 M HCl-0.1 M HF. The performance of this technique was evaluated by separating these elements from two terrestrial and two extraterrestrial samples. The recovery yields for Mo, W, Zr, and Hf were nearly 100% for all of the examined samples. The total contents of the Zr, Hf, W, and Mo in the blanks used for the chemical separation procedure were 582, 9, 29, and 396 pg, respectively. Therefore, our new separation technique can be widely used in various fields of geochemistry, cosmochemistry, and environmental sciences and particularly for multi-isotope analysis of these elements from a single sample with significant internal isotope heterogeneities.