The traditional single base station GNSS deformation monitoring system is greatly influenced by the base station stability and data quality. In order to improve the accuracy and reliability of monitoring system, this paper develops a new method of real-time kinematic relative positioning based on multiple base stations and multi-GNSS. Aiming at the problem of weight allocation of multiple base station and different GNSS, the idea of Helmert variance component estimation and robust estimation are introduced. Through a real example analysis, the robust variance component weighting method is more efficient and reliable than the traditional range-based (baseline length) weighting method for different base station and empirical weighting method for different GNSS. The accuracy of the deformation monitoring of the proposed method is higher and more reliable than those of single base station with GNSS or multi-GNSS.