We investigated the effect of encapsulation on poly(3-hexylthiophe) (P3HT) bottom-gate field-effect transistors (BG-FETs) with a high on/off current ratio achieved by thermal annealing in N2 atmosphere. The intensity of the oxygen-related absorption peak in the Fourier-transform infrared (FT-IR) spectra of the P3HT films showed a correlation to the on/off current ratio of the FETs. In order to eliminate this oxygen-doping effect, we evaluated three types of encapsulation film: polymer insulator, SiNx, and polymer-SiNx hybrid insulator. We found that the polymer-SiNx hybrid insulator film can suppress both damage caused by the formation of the encapsulation layer and the doping caused by exposure to air. To investigate the effect of encapsulation, we calculated the time dependence of the unintentional dopant density of the P3HT film.