When a satellite can not be saw by all the stations, time transfer between the satellite clock and the system time can but be accomplished by satellite. We need predict clock error for receiving continuous satellite clock error. This paper thoroughly study on satellite clock error prediction methods based on short arc tracking when the satellite can not be saw high frequency by all the stations. A hybrid model combining polynomial and AR model is proposed. By calculation and analysis using GPS Satellite Clock Error, some useful conclusions are drawn by comparing the results with that calculated from the classical quadratic polynomial model. In the short-term(from 8 to 20 hours) predicting GPS satellite clock error precisions of the hybrid method are up to 1 ns, which exceeds quadratic polynomial model obviously and satisfies precision requirements in the real application. This conclusion can be an academic base of satellite clock error predicting when the satellite can not be saw high frequency by all the stations.