Using molecular dynamics (MD) simulations, the transition of the plastic deformation mechanism of Ti-Nb alloys during the tensile process was studied, and the effects of temperature, Nb composition, and strain rate on the deformation mechanism were also investigated. The results show that the deformation process of Ti-Nb alloys involves defect formation, followed by twinning and ω-phase transition, and ultimately, dislocation slip occurs. The <111>{112} slip makes the ω-phase easily overcome the transition energy barrier, inducing the phase transition in the twinning process. Increasing temperature will enhance the plasticity and reduce the strength of the material, while increasing Nb composition will have the opposite effect on the deformation. The simulations show a competition between twinning and dislocation slip mechanisms. With the increase in Nb content, the plastic deformation mechanism of the alloy will change from twinning to dislocation slip. In addition, the plastic strain range increases with the increase in the deformation rate in Ti-Nb alloys. At a higher strain rate, the alloy’s plastic strain range is affected by various deformation mechanisms, which significantly influence the plasticity of the material. The findings of this study provide further insights into the design of Ti-Nb-based alloys.