Separation of vanadium from molybdates is an essential task for processing the leaching solution of hazardous spent hydrodesulphurization (HDS) catalyst. In this study, the difference in the main naturally occurring mineral forms of Mo and V inspired us to develop a method for the deep removal of V from molybdate solution using Fe₃O₄ as an adsorbent. First, the adsorbent was synthesized with coprecipitation method, and then it was characterized by XRD, TEM, and VSM. The synthesized material consisted of pure Fe₃O₄ nanoparticles that exhibited paramagnetic property, with a saturated magnetization of 68.6 emu g⁻¹. The V removal efficiency was investigated using batch adsorption experiments in varying conditions. Results indicated that V could be deeply removed from various concentrations of molybdate solution at pH of 7.0–11.0 within 5 min. A slight decrease was found in the adsorption ratio after the adsorbent had been reused for 4 cycles. The resulting molybdate solution contained less than 0.02 g L⁻¹ of V, which satisfies the requirement for preparing high-quality products. Finally, a process flowchart is presented for the separation of Mo and V from the leaching solution of spent HDS catalyst, based on the excellent V removal performance and rapid separation rate of the Fe₃O₄ adsorbent.