Uniaxial deformations of amorphous poly(lactic acid) (PLA) films were performed at two different temperatures, 70 and 80 °C, at various draw strains. The samples deformed at 70 °C showed a strain-induced mesophase, and the structural ordering and thermal stability increased as the draw strain increased. Further annealing was performed in situ at constant length at the drawing temperature of 70 °C for the films drawn to strains of 100% and 230%. Unusually, we found that after annealing, the crystal structure of the film at lower strain was more ordered than the one at higher strain. Further investigations revealed that upon annealing the structural evolution followed a distinct molecular mechanism for the samples stretched to the two draw strains. For the sample drawn to 100%, the mesophase melted very quickly upon annealing, resulting in chain randomization and the release of the constraints on the thermodynamic relaxation of the oriented amorphous chains. The chain relaxation motions had a beneficial effect on the occurrence of the conformational rearrangements that are necessary for crystalline ordering. By contrast, for the 230% sample, the melting of the mesophase was slow and most of the chain orientations were preserved upon annealing. As a result, a less ordered crystal structure was formed since the local relaxation motions that are necessary for promoting crystalline order via conformational rearrangements were hindered.