The heat treatment of an injection-molded polyoxymethylene slightly below the melting point and subsequent isothermal treatment at 130°C were performed. The polyoxymethylene structure was examined using field-emission scanning electron microscopy and polarization infrared reflection measurements. After the heat treatment, a significant change in the surface morphology was observed, and the reflection spectrum derived from the polariton in the injection direction also changed dramatically. Since the reflection spectrum in the injection direction contains the reflection component of the perpendicular direction and vice versa, the polarization spectra of both directions can be calculated consistently. The mixing ratio of each crossed component and the pure relative permittivity both parallel and perpendicular to the main-chain direction were determined using the oscillator model. The heat treatment reduced the ratio of the perpendicular component and increased the order structure until just before melting. The structural changes characterized by the two techniques, along with Raman spectroscopy and differential scanning calorimetry, are discussed.