Calibrating the global navigation satellite system (GNSS) time–frequency transfer system is crucial for accurate GNSS time–frequency transfer. The most commonly used relative calibration method relies on the common-clock to eliminate clock differences. However, it cannot eliminate the changes in clock signal reference point delay (REFDLY). The changes in REFDLY during calibration could not be ignored, especially for ordinary users in an unstable environment. To address this issue, we use the GNSS real-time single-difference time synchronization calibration based on clock-steering, which can detect the change in REFDLY. According to this method, the clock differences and REFDLY are eliminated simultaneously. We installed two GNSS antennas on the roof of the Xinghu Building of Wuhan University and designed a clock synchronization terminal to evaluate the performance of this method. The data were collected on Day of Year 152–156, 167–171, 222–226, 231–235, 244, 258, 260, and 262 in 2022. In accordance with the calibration results, the standard deviation better than 100 ps, and the stability reaches 10−15@10000s . Also, the time variance better than 60 ps, and the uncertainty uCAL better than 0.5 ns. Compared to the common-clock calibration, one of the most significant benefits is the elimination of REFDLY, which leads to decreased uncertainty and better stability over both the short-term and long-term.