Organic field-effect transistors (OFETs) based on p-channel polymer semiconductors such as poly(3-hexyl)thiophene (P3HT) and 30-diketopyrrolopyrrole-selenophene vinylene selenophene (30-DPP-SVS) were fabricated using a microwave (MW) irradiation process for thermal annealing. The influence of MW annealing was investigated based on microstructural characterizations such as X-ray diffraction (XRD) and atomic force microscopy (AFM). MW annealing not only shortened the annealing time, but also produced enhanced device performance including higher on/off ratio, lower threshold voltage, and higher field-effect mobility in comparison with the traditional annealing method. These microstructural analyses revealed that annealing by MW irradiation enhances the crystallinity and molecular orientation in the polymer thin films in a short time, thereby improving the electrical performance effectively. Our results suggest that MW-assisted annealing is a simple and viable method for enhancing OFET performance.