Isothermal compression of near alpha Ti-5.6Al-4.8Sn-2.0Zr alloy is conducted on a Thermecmaster-Z simulator at the deformation temperatures ranging from 1173 K to 1333 K, the strain rates ranging from 0.001 s-1 to 10.0 s-1 at an interval of an order magnitude and the height reductions ranging from 50% to 70%. The primary grain size is measured at an OLYMPUS PMG3 microscope with the quantitative metallography SISC IAS V8.0 image analysis software. A multi-scale constitutive model coupling the grain size, volume fraction and dislocation density is established to represent the deformation behavior of near alpha Ti-5.6Al-4.8Sn-2.0Zr alloy in high temperature deformation, in which the flow stress is decomposed a thermal stress and an athermal stress. A Kock-Mecking model is adopted to describe the thermally activated stress, and an athermal stress model accounts for the working hardening and Hall-Petch effect. A genetic algorithm (GA)-based objective optimization technique is used for determining material constants in this study. The mean relative difference between the predicted and experimental flow stress is 5.98%, thus it can be concluded that the multi-scale constitutive model with high prediction precision can efficiently predict the deformation behavior of near alpha Ti-5.6Al-4.8Sn-2.0Zr alloy in high temperature deformation.