The continuous solvent extraction operations for the removal of molybdenum from ammonium tungstate solution was conducted using a solvent extraction system consisting of 10% (v/v) N263 as extractant and 30% (v/v) isooctanol as modifier in sulfonated kerosene for 63 h under optimized conditions in mixer-settlers. The concentration of Mo in raffinate was less than 10 mg/L with mass ratio of Mo/WO3 less than 6.0 × 10−5 and the concentration of Mo in strip liquor reached 30 g/L with mass ratio of WO3/Mo less than 1.0 × 10−2, which was consistent with the results of batch tests. The loaded organic solution and the oxidized organic solution were characterized by infrared spectroscopy and the results demonstrated that molybdenum exists in the form of [Mo2O11(H2O)2]2− in oxidized organic solution. The theoretical calculation of temperature change of the organic solution in oxidation process was conducted. The oxidant of 7 wt% H2O2 was recommended to be used during industrial production and a cooling water system has to be installed around the oxidation tank at the same time.The new process exhibited significant advantages of low overall costs, large value increase due to molybdenum producibility of MSA and environmental friendliness without wastewater and residue generation.