The effects of initial microstructure on the flow stress, strain rate sensitivity (m), strain hardening exponent (n), apparent activation energy (Q) for deformation of Ti–5Al–2Sn–2Zr–4Mo–4Cr alloy were investigated using isothermal compression tests. Results show that the alloy with Widmanstätten alpha plates shows a higher peak stress and flow softening. Additionally, the alloy with equiaxed primary alpha exhibits an early yield drop at or above 810 °C and at strain rates of 0.1–5.0 s−1. In the strain range of 0.5–0.7, m of the alloy with equiaxed primary alpha is found to be larger at 0.01 s−1 and lower deformation temperatures. This phenomenon could be reasonably explained based on the microstructure evolution. The strain has a significant effect on n of the alloy with Widmanstätten alpha plates, which is attributed to platelet bending/kinking and dynamic globularization of α phase. In the strain range of 0.15–0.55, Q of the alloy with Widmanstätten alpha plates is larger.