Molybdenum (Mo) and vanadium (V) are both important strategic metals. Due to their similar physicochemical properties, it is always a challenge to realize their deep separation from a solution. However, based on the valence difference of Mo and V, this task can be achieved by the selective complexation precipitation of hexamethylenetetramine (HMT). In this study, through precipitation behavior studies in the single metal species solutions and the mixed species solutions of Mo and V in different chemical valence states, the complexation precipitation separation system of V and Mo was constructed. As a result, in the single metal species solution, the precipitation depths of Mo(V), Mo(VI) and V(V)) reached 96.83% 98.77% and 99% under the best conditions, respectively, while V(IV) remained in the solution. The results of the mixed-species complexation precipitation experiments revealed the most efficient selective separation scheme by HMT. Furthermore, combined with the characterization of the complexation precipitates of HMT with the single species of Mo(V), Mo(VI) and V(V), the mechanisms of the complexation reactions were elucidated. In particular, due to the different ion species of Mo caused by the different valence states, the complexation precipitation mechanisms of Mo(V) were different from those of Mo(VI). Finally, the differences in the mechanisms of Mo(V), Mo(VI) and V(V) complexation were also presented in their kinetics, and the reaction constants and activation energies were calculated by first-order kinetics. This study may provide further insight into the selective complexation separation of Mo and V.