The formation and distribution of mesophase in ethylene vinyl alcohol copolymer ultrasonic micro-injection-molded at different mold temperature and filling velocity were investigated using wide angle X-ray diffraction (WAXD) technique and dynamic rheological characterizations. The one-dimensional WAXD profiles of unoriented and oriented components was separated to evaluate the fraction of mesophase, orthorhombic crystals and amorphous phase in each part. The results demonstrated that mesophase mostly existed in samples with mold temperature lower than 90 °C. Compared to the mold temperature, the filling velocity had slight influence on the formation of mesophase. With the WAXD mapping experiments along the thickness direction, it was found that mesophase mainly appeared in the core layer of unoriented component, regardless of mold temperature and filling velocity. The formation of the mesophase is found to depend on the competition between the time needed for polymer chain relaxation and crystallization. Only the polymer chains relaxed to a random coil state in the core layer is possible to form mesophase, otherwise polymer chains will crystallize into orthorhombic crystals.