The formation and distribution of different crystal forms in ultrasonic microinjection-molded poly(butylene 2,6-naphthalate) (PBN) samples prepared using different mold temperatures were investigated by microfocus wide-angle X-ray diffraction (WAXD), differential scanning calorimetry (DSC) and polarized-light optical microscopy (POM). The relative fractions of liquid-crystalline (LC) mesophase, α-phase and β′-phase along the thickness direction of microinjection-molded samples were obtained via a decomposition of the WAXD curves. The results indicate that the mold temperature affects the formation of the LC mesophase and α-crystals, but not the formation of β′-crystals. Moreover, the LC mesophase and α-phase were detected in both skin and core regions of the microinjection-molded PBN samples, while the β′-crystals were only observed in the skin layer. In the heating process, the crystals in the core region and skin layer began to melt at temperatures of about 240 and 250 °C, respectively, which is consistent with the different thermal stabilities of the α- and β′-phases. It is inferred that the β′-phase is able to form under a certain high shear flow, implying that the polymorphic structure of injection-molded parts of PBN can be tailored by variation of the molding conditions. • PBN tensile bars were prepared using an ultrasonic microinjection-molding machine. • The LC mesophase and α-phase were detected in both skin and core regions. • The β′-crystals were only observed in the skin layer. • Formation of β′-phase is influenced more by the shear flow than by the cooling rate. • Polymorphic structure of PBN can be tailored by variation of the molding conditions.