Crystallizable glassy polymers can undergo multistage structural evolutions and form multiple types of ordered phases (e.g., mesomorphic and crystalline phases) during stretching below their glass transition temperatures (Tg). However, the structural evolution of polymers during sub-Tg stretching and the associated molecular mechanisms have not been well understood. In this work, we investigated the multistage structural ordering of glassy polymers and the related mechanisms during stretching below Tg by studying poly(trimethylene terephthalate) (PTT) as a model system. Roles of chain orientation and conformational transition on the multistage structural evolution of melt-quenched PTT were elucidated through a loading?unloading experiment. When stretched below Tg (e.g., 25 °C), the orientation of polymer chains and the stacking of phenylene rings lead to an intermolecular ordering, which induces the generation of a smectic C-like mesomorphic phase. The orientation degree of chains in such a mesomorphic phase increases with further stretching. This highly oriented mesomorphic phase transforms into a triclinic crystalline phase when the applied stress is unloaded. Stretching at a higher temperature (e.g., 40 °C) results in the formation of a more ordered mesomorphic phase and facilitates the induced crystallization due to the enhanced chain mobility. Fourier transform infrared results demonstrated that the unloading-induced crystallization of stretched PTT is originated from the trans-gauche conformational transition.