Molybdenum is harmful and useful. The efficiency of molybdenum trade effluent treatment is low and it is difficult to extract and recycle. To solve this problem, a novel membrane chemical reactor with mixed organic-water solvent(MCR-OW) had been used for the investigation of impact factors on the migration characteristics of Mo(VI) in the simulated trade effluent. The novel MCR-OW contains three parts, such as feeding pool, reacting pool and renewal pool. Flat membrane of polyvinylidene fluoride(PVDF) membrane was used in the reacting pool, the mixed solutions of diesel and NaOH with N, N′-di(1-methyl-pentyl)-acetamide(N-503) as the carrier in the renewal pool and the simulated trade effluent with Mo(VI) as feeding solution. The influencing factors of pH and the ion strength in the feeding solutions, the volume ratio of diesel to NaOH solution and N-503 concentration in the renewal solutions were investigated for the testing of the migration efficiency of Mo(VI). It was found that the migration efficiency of Mo(VI) could reach 94.3% in 225 min, when the concentration of carrier(N-503) was 0.21 mol/L, the volume ratio of diesel to NaOH in the renewal pool was 4:3, pH in the feeding pool was 3.80 and the initial concentration of Mo(VI) was 2.50 × 10−4 mol/L. Moreover, the stability and feasibility of MCR-OW were discussed according to Mo(VI) retention on the membrane and the reuse of the membrane.