A face-on oriented thin film of poly(3-hexylthiophene) (P3HT) is suitable for an organic semiconductor layer in a photovoltaic device, and thus analysis of the film structure in terms of molecular orientation is crucial. Although the face-on film often has a poor crystallinity, diffraction techniques have long been employed for the structural analysis, and only very minor crystal parts have been discussed. In our previous study, P3HT was revealed to have a uniquely oriented structure even in an amorphous film by using p-polarized multiple-angle incidence resolution spectrometry (pMAIRS), which is powerful to analyze the molecular orientation, crystallinity, and the conjugation length of P3HT. With the best use of the potential of pMAIRS, in the present study, the controlling mechanism of the molecular orientation of P3HT correlated with the crystallinity in a spin-coated thin film is revealed. As a result, by employing a high-spin speed at 8000 rpm, a highly face-on oriented thin film having a very low crystallinity is obtained, which readily reveals that the face-on component has a strong correlation with the amorphous aggregates.