In dual-antenna interferometric synthetic aperture radar system, the reference phase was usually estimated by joint calibration with transferring corresponding points for the scene without ground control points, which is too time-consuming. To solve the problem, the factors influencing the reference phase were analyzed. The analytic formula was given, and simulation was done according to the system parameters. The height error caused by reference phase was analyzed. According to the analysis results, the high precision realtime reference phase estimating algorithm was presented, combined with the extern coarse precision elevation, the filtered interferometric phase and coherence. The detailed flow of the algorithm was given. The processing results of the real data from airborne dual-antenna interferometric synthetic aperture radar system validate that a 2 m relative elevation precision can be achieved with the system in the paper by the algorithm presented, and the estimated speed can reach more than 20 times faster when processing the data of 4096×6560pixel.