Three functional models, polynomial, spectral analysis, and modified AR model, are studied and compared in fitting and predicting clock deviation based on the data sequence derived from two-way satellite time and frequency transfer. A robust equivalent weight is applied, which controls the significant influence of outlying observations. Some conclusions show that the prediction precision of robust estimation is better than that of LS. The prediction precision calculated from smoothed observations is higher than that calculated from sampling observations. As a count of the obvious period variations in the clock deviation sequence, the predicted values of polynomial model are implausible. The prediction precision of spectral analysis model is very low, but the principal periods can be determined. The prediction RMS of 6-hour extrapolation interval is 1ns or so, when modified AR model is used.