By simultaneously estimating satellite clock drifts (SCDs) as either constant parameters or piece-wise parameters, we present an improved integrated orbit determination and time synchronization approach for BDS-3 satellites with raw inter-satellite link (ISL) observations. Experiments with L-band data from seven monitoring stations in China and ISL data from eight satellites of the third-generation Beidou Navigation Satellite System (BDS-3) were carried out and the two SCD estimation strategies are validated. It is demonstrated that, with SCDs estimated, the quality of orbits and clock offsets is comparable to those with SCDs corrected using predicted values. The accuracy of the estimated orbits and clocks are up to 0.019 m (radial) and 0.095 ns, respectively, with improvements of 95% and 90%, when compared with the results using the L-band data alone. It is also demonstrated that estimating SCDs time slice by time slice is slightly worse in accuracy but superior in coping with possible frequency jump of satellite clocks.