The modernized GPS, Galileo, and BeiDou global navigation satellite system (BDS3) offers new potential for time transfer using overlap-frequency (L1/E1/B1, L5/E5a/B2a) observations. To assess the performance of time and frequency transfer with overlap-frequency observations for GPS, Galileo, and BDS3, the mathematical models of single- and dual-frequency using the carrier-phase (CP) technique are discussed and presented. For the single-frequency CP model, the three-day average RMS values of the L5/E5a/B2a clock difference series were 0.218 ns for Galileo and 0.263 ns for BDS3, of which the improvements were 36.2% for Galileo and 43.9% for BDS3 when compared with the L1/E1/B1 solution at BRUX–PTBB. For the hydrogen–cesium time link BRUX–KIRU, the RMS values of the L5/E5a/B2a solution were 0.490 ns for Galileo and 0.608 ns for BDS3, improving Galileo by 6.4% and BDS3 by 12.5% when compared with the L1/E1/B1 solution. For the dual-frequency CP model, the average stability values of the L5/E5a/B2a solution at the BRUX–PTBB time link were 3.54∙× 10−12 for GPS, 2.20 × 10−12 for Galileo, and 2.69 × 10−12 for BDS3, of which the improvements were 21.0%, 45.1%, and 52.3%, respectively, when compared with the L1/E1/B1 solution. For the BRUX–KIRU time link, the improvements were 4.2%, 30.5%, and 36.1%, respectively.