The time-varying biases within carrier phase observations are integrated into satellite clock offset parameters for precise clock estimation. Consequently, when the precise satellite clock bias is applied to the third frequency observation for precise point positioning (PPP), a new type of inter-frequency clock bias (IFCB) with satellite dependence should be noticed. If the IFCB is estimated together with the receiver coordinates, tropospheric wet delay, ambiguity and other parameters, it will increase the computational burden and lead to more time consumption. In order to solve this problem, the IFCB of GPS Block IIF satellites were estimated using 162 global uniformly distributed Multi-GNSS Experiment (MGEX) stations. By analyzing the time-varying characteristic of each satellite IFCB and combining the lag characteristics of the final ephemeris products, a modeling method of short-term IFCB prediction based on the epoch-by-epoch sliding Pearson autocorrelation function is proposed. The feasibility of this method was verified through the Student’s t-distribution, comparison with the measured IFCB, the posteriori residual of the third frequency carrier phase and the kinematic/static PPP solutions. The results showed that since the IFCB period was not a complete 24 h, the difference in the IFCBs time series on different days was increasingly significant with the passage of lag time, and the correlation constantly decreased. The peak-to-peak amplitudes of the IFCB difference reached 1.13, 3.44, 6.86 and 11.25 cm when the lag time was 1, 9, 19 and 29 days, respectively. In addition, based on the lag characteristic of final precise ephemerides released by the International GNSS Service (IGS) analysis centers, the prediction accuracy of the IFCB was evaluated with a time lag of 7 days. The root mean square of the posteriori residuals at the third-frequency observation decreased by approximately 51.3% compared to that without considering for IFCB correction. The triple-frequency uncombined PPP in the horizontal and vertical directions improved by approximately 33.2% and 17.2% for the static PPP solutions and 50.2% and 39.7% for the kinematic PPP solutions, respectively. In general, the accuracy and convergence time of the triple-frequency uncombined PPP were equivalently improved when the predicted IFCB and the measured IFCB were used.