Deep separation of tungsten from molybdenum has become a bottleneck in molybdenum metallurgy, especially in high-chloride aqueous systems, because of competitive extraction. A new primary amine extractant, 3-(nonyloxy)propane-1-amine (NNA), was designed and synthesized to separate tungsten and molybdenum. Over 96% extraction efficiency of tungsten was achieved by NNA with the optimal conditions, with the saturated capacity exceeding 55 g/L. Meanwhile, a high separation coefficient of 40 for W to Mo was obtained by single-stage extraction. The extraction mechanism of different NNA concentration ranges was determined based on the H+–MoO42––WO42– aqueous system. The extraction order was Mo3W4O246–, Mo2W5O246–, and [WO42–, MoO42–], with the stoichiometric numbers of NNA determined as 8, 8, and 1, respectively. Remarkably, NNA exhibited good performance in high-chloride aqueous systems. The separation coefficient toward W over Mo was greater than 3.00 × 104 with a three-stage countercurrent extraction. In conclusion, NNA has a tremendous potential application value for tungsten and molybdenum separation, especially in complex systems.