The shearing effects of sheared polymer melts on their finally formed crystalline structures of poly(L-lactide) (PLLA) were investigated by means of small angle X-ray scattering (SAXS) and wide angle X-ray diffraction (WAXD). The results of WAXD prove that shear has no effects on the crystal structure of PLLA. The SAXS results demonstrate that both of the long period and the thickness of crystalline lamellae increase with rising shear rates when vertical to the shear direction, but remains constant when being parallel to the shear direction. The structural changes for samples prepared with different shear temperature or under the same shear strain but different shear rate were investigated. The mesophase of polymer melts and shearing effects on their pre-ordered phase turned out to be the key factor affecting the crystal structure of PLLA under different shearing conditions.