In this study, molecular dynamic simulation was used to investigate the evolution of microstructure and dislocation configuration of pre-strain Ti2AlNb-based alloy under electric current treatment (ECT). Three bicrystal models embedded with equiaxed α2 particle with different initial orientations and three tensile pre-strain ( \(\varepsilon \hspace{0.17em}\) = 0.021, 0.08 and 0.106) were built, and the equivalent electron-wind force was applied on each model to indirectly simulate the athermal electroplastic effect. The results show that the ECT increases the proportion of BCC phase by up to 30% except for the \(\varepsilon \hspace{0.17em}\) = 0.021 condition and eliminates the sub-grain boundaries formed during pre-straining. The increasing dislocation density in BCC structure and opposite situation in HCP structure narrows the gap in electric conductivity between the BCC phase and the HCP one and contributes to the decline of absolute value of electric energy ∆Ge and therefore decelerates the HCP → BCC phase transformation until reaching an equilibrium state with the proceeding of ECT process. Moreover, the electron-wind force induces annihilation in defect-rich areas and activates the merging of partial dislocations. It also brings about local stress concentration on phase boundary and promotes \(\left\{ {3\overline{2}1} \right\}001\) and \(\left\{ {201} \right\}0\overline{2}1\) twin variants. This work helps to deepen the understanding of pure electroplastic effect in titanium alloys during ECT process.