The influence of different shear stresses induced by changing injection molding speeds on molecular chain orientation and lamellar branching of beta-nucleated iPP/poly(ethylene terephthalate) (PET) microparts was investigated using two-dimensional wide-angle X-ray diffraction and 2D-small-angle X-ray scattering. Results indicated that the prevailing shear stress can promote the formation of parent-daughter alpha-crystal structure and twisted shish-kebab structure in subsequent microparts. The diffraction of (300) plane of beta-crystals was also observed at varying injection speeds. Increasing injection speeds can significantly enhance the content of beta-crystals from 24 to 41% for beta-nucleated iPP microparts. Additionally, the content of beta-crystals was further enhanced in beta-nucleated iPP/PET microparts with in situ formation of PET microfibrils under intensive shearing conditions. The addition of both PET and beta-nucleation agents coupling with high shearing conditions exerts a synergetic effect on the development of beta-crystals. However, the orientation degree of crystal lattice decreased with increasing injection speeds for both beta-nucleated iPP and iPP/PET microparts.