The common view time transfer and two-way time and frequency transfer methods are currently the main means for achieving time synchronisation at nanosecond level. However, these methods have some limitations in real time and cost, which limit their wide applications in many fields, such as time synchronisation among base stations of the upcoming 5G network. In order to meet the requirements of nanosecond time synchronisation, a low-cost differential timing method is proposed in this paper by changing the manner of generation of traceability model parameters in GNSS navigation messages. The time deviation between GNSS system time and the timing laboratory that maintains Coordinated Universal Time (UTC) kept by timing laboratory named k (UTC(k)) is monitored by receiving the GNSS signal in space with monitoring receivers. The new traceability model parameters are generated with the monitored time deviations and then broadcast to users through the GNSS navigation message. The precision of the one-way timing method can be improved from tens of nanoseconds to the order of several nanoseconds with the proposed method. In addition, there are obvious advantages to carry out this method on the geostationary satellites in the BeiDou navigation satellite (BDS) constellation. The proposed method is verified on an experimental platform based on the UTC(NTSC) time frequency signal and the geostationary satellites in the BDS-3 constellation.