The pyramid wavefront sensor (PWFS) is a novel wavefront sensor with several inspiring advantages compared with Shack-Hartmann wavefront sensors. The PWFS uses four pupil images to calculate the local tilt of the incoming wavefront. Pupil images are conjugated with a telescope pupil so that each pixel in the pupil image is diffraction-limited by the telescope pupil diameter, thus the sensing error of the PWFS is much lower than that of the Shack-Hartmann sensor and is related to the extraction and alignment accuracy of pupil images. However, precise extraction of these images is difficult to conduct in practice. Aiming at improving the sensing accuracy, we analyzed the physical model of calibration of a PWFS and put forward an extraction algorithm. The process was verified via a closed-loop correction experiment. The results showed that the sensing accuracy of the PWFS increased after applying the calibration and extraction method.