The Bayan Obo ore deposit is a world-renowned polymetallic coexistence mine that integrates important elements, such as rare earths, iron, niobium, and titanium. The chemical properties of niobium and titanium are similar, and the two often coexist in the Bayan Obo deposit as isomorphs, making them difficult to separate. Therefore, the separation of niobium and titanium is crucial for the efficient utilization of niobium resources in the Bayan Obo ore deposit of China. To discuss the feasibility of separating niobium and titanium by selective electrolysis, cyclic voltammetry and square wave voltammetry were used to study the reduction mechanism of niobium oxide and titanium oxide in NaF–Na3AlF6 molten salt. The results revealed significant differences in the diffusion coefficients and reduction steps of Nb5+ and Ti4+ during reduction at a molybdenum cathode. At 950 °C, the diffusion coefficient of Nb5+ during reduction at a molybdenum cathode was 3.57 × 10–6 cm2/s. Also, in the NaF–Na3AlF6 system, Nb5+ underwent a three-step reduction as follows: Nb(V)→Nb(IV)→Nb(I)→Nb. The diffusion coefficient of Ti4+ during reduction at the molybdenum cathode was 9.92 × 10–7 cm2/s, and Ti4+ underwent a two-step reduction in the NaF–Na3AlF6 system: Ti(IV)→Ti(I)→Ti. When Nb2O5 and TiO2 were both present in the NaF–Na3AlF6 system, the deposition potential of niobium metal (−0.64 V) differed from that of titanium metal (−0.77 V). These differences in diffusion coefficient, reduction step, and deposition potential enabled selective electrolytic separation of niobium and titanium.