The morphology and properties of poly (3-hexylthiophene) (P3HT) thin films after femtosecond laser irradiation with various fluences were studied. Two types of final ablation morphology were characterized through optical microscope (OM), atomic force microscope (AFM) and scanning electron microscope (SEM). At lower fluences, nano-bumps were formed in the central area. At higher fluences, nano-bumps were formed in the entire irradiated area and the material in the center disintegrated. Time-resolved pump–probe system was used to investigate laser − P3HT ultrafast interaction and the principle of morphological differences, which revealed that the Coulomb explosion was the reason for the morphology change with fluence increasing. Photoluminescence (PL) spectra indicated that the transition of the PL signal from enhancement to quenching with various laser fluences was related to the effect of laser on morphology and molecular exciton. A maximal 2 fold lifetime enhancement of bound polaron pair dissociation and 1.3 fold lifetime improvement of defect trapping were achieved at higher fluences, which contributed to obtaining more effective free carriers and subsequent photocurrent. These results promote the potential applications of femtosecond laser on P3HT and other organic semiconductors, especially organic photovoltaics (OPV) devices.