Astronomical refraction in pointing error of large radio telescope was considered. An astronomical refraction model using real-time measured temperature, pressure and relative humidity was newly applied to pointing error calibration model. A simulation was used to compare traditional and real-time astronomical refraction model in different weather conditions. This calibration model was applied to pointing calibration of Shanghai Tianma 65 m Radio Telescope. The Ku-band experiment showed that the real-time astronomical refraction model is better than the traditional model. Pointing accuracy is 25.8% better under elevation of 20°, 45% better under elevation of 15° and 60% better under elevation of 10°. Pointing accuracy is 5.0″, which is 5.3% better than traditional model. The worsening of pointing accuracy at low elevation caused by astronomical refraction is basically removed.