Relative to single Global Navigation Satellite System (GNSS) measurements, i.e., the measurements from a single GNSS system, a single GNSS code, and a single GNSS receiver, multi-GNSS measurements for time transfer could improve reliability and provide better short-term stability. Previous studies applied equal weighting to different GNSS systems or different GNSS time transfer receivers, which, to some extent, revealed the improvement in the additional short-term stability from the combination of two or more kinds of GNSS measurements. In this study, the effects of the different weight allocation for multi-measurements of GNSS time transfer were analyzed, and a federated Kalman filter was designed and applied to fuse multi-GNSS measurements combined with the standard-deviation-allocated weight. Tests with real data showed that the proposed approach can reduce the noise level to well below about 250 ps for short averaging times.