With a decline in high-grade molybdenum reserves, the development of other types of molybdenum resources have received increasing attention. Vanadium shale is a multi-metal shale and fine-grained sedimentary rock comprising small grains and various minerals. After leaching and extracting vanadium, the solution often contains a low concentration of molybdenum. However, because of the low molybdenum concentration, many processing plants treat it as an acidic wastewater, which wastes molybdenum resources and carries the risk of environmental pollution. The leaching process of vanadium shale mostly involves high-temperature and high-pressure operations, which greatly increase the content of impurity ions such as aluminium and phosphorus in the pregnant leach solution. These impurity ions increase the difficulty in separating and recovering molybdenum. In this study, the adsorption and separation of molybdenum at leach liquor of low molybdenum concentration were investigated. The effects of different factors such as: (i) pH of feed solution, (ii) adsorption time, and (iii) presence of impurity ions, aluminium and phosphorus, on the adsorption and separation of molybdenum using five different anion-exchange resins, D201, D296, D301, D314, and D301R, were investigated. The static adsorption and desorption test results showed a molybdenum adsorption capacity of 222 mg/g at pH = 1.5 by the D301 resin. The desorption efficiency using 20% NH₄OH was 96.1%. The adsorption efficiencies of aluminium and phosphorus were 1.31% and 3.10%, respectively. This is a better choice for separating molybdenum from complex solutions. The experimental results from spectra and theoretical calculations showed that the -NH group of D301 resin was combined with the O atoms of MoO3·3H2O, Al(SO4)2−, and H2PO4− by electrostatic attraction. The binding energies of these three species were − 311 kJ/mol, −231 kJ/mol, and − 62.0 kJ/mol respectively, indicating that D301 resin preferentially adsorbed MoO3·3H2O. Based on the above results, the D301 resin can adsorb molybdenum(VI) in complex solutions under low pH conditions, and this study is expected to promote the comprehensive recovery of valuable metals from vanadium shale.