Semicrystalline polymers generally undergo polymorphic crystal transition and lamellae structural changes during stretching deformation. Such stretch-induced multilevel microstructural evolutions are more complicated in the case of random copolymers due to the low crystallinity and less regular crystal structure. Herein, we choose the poly- (butylene adipate-ran-terephthalate) (PBAT), a representative commercially available and flexible biodegradable polyester, as a model system and report its polymorphic crystal transition and lamellae evolution during stretching. Both the lamellae evolution and crystal transition of PBAT depend strongly on the crystallization and deformation temperatures (Tc and Td) due to the effects of stability of original crystals and the mobility of polymeric chains. The original lamellae of PBAT change into the chain-extended fibrillar lamellae during stretching via the melt-recrystallization mechanism; this process is delayed with increasing Tc because of the improved crystal stability. PBAT undergoes α-to-β crystal transition during stretching; the crystal transition is governed by the orientation degree and favored at low Tc and Td. The crystal transition takes place in the newly formed chain-extended crystals rather than the original crystals. The transformed β crystals can recover to their α counterparts upon annealing at high temperature when the stress is released.