The two-way satellite time and frequency transfer (TWSTFT) is a precise time transfer technique and has being used to generate the international atomic time since 1999. Nowadays, TWSTFT links have formed a worldwide network and the large amount of TWSTFT data become highly redundant. To fully utilize the data of TWSTFT network and improve the TWSTFT results, a feasible method of processing data is proposed in this paper. According to the stability of each link, we assign a weighting value to each related equation and then solve the matrix equation with the weighted least squares method. We perform data analysis with practical time transfer data, and the results show that it is an effective method to improve the short-term stabilities and uncertainties of TWSTFT results.