Aiming at the problem of inconsistent delay of the uplink and downlink in a railway time synchronization network, a compensation scheme based on the enhanced algorithm for real-time calculation of data package queuing delay (ERTCQD) is proposed in this work. First, based on the transmission link delay, the clock model of a railway time synchronization network is obtained. Second, considering that the calculation parameters of clock frequency difference in the real-time calculation algorithm of data package queuing delay are difficult to obtain and the clock frequency difference will lead to linear shift of delay with time, the calculation method is improved by calculating the linear clock frequency difference, and the queuing delay is estimated by solving the queuing delay minimum data package. Finally, the queuing delay is introduced into the clock model, and a new clock offset estimation method is obtained, which can improve the time accuracy degradation caused by delay asymmetry. The results show that: the ERTCQD algorithm has higher accuracy, and the average error is 0.22 ms. The compensation effect of this scheme is good. Compared with results before compensation, the clock offset error is reduced by 73.2%, and the link delay asymmetry is reduced by 94.2%. The proposed scheme significantly improves the timing accuracy and provides a new reference for solving the delay asymmetry of the railway time synchronization network.