The position service provided by global satellite navigation system (GNSS) has high-precision characteristics, it is widely used in the field of building deformation monitoring. As the baseline between the receivers is short for the above application scope, the common clock source method can be used to eliminate some error items. For common clock SDCP measurement, the uncalibrated phase delay is a major error item. The UPD feature and the usual estimation methods were analyzed and verified by experimental tests in the paper. The experimental results testify that the UPD is a random variable, which varies with the ambient temperature. The UPD can be eliminated by using ARMA filter, and the ARMA filtered SDCP position accuracy can be improved by more than 20% compared to the DDCP positioning result.