The core of eLoran ground-based timing navigation systems is the accurate measurement of groundwave propagation delay. However, meteorological changes will disturb the conductive characteristic factors along the groundwave propagation path, especially for a complex terrestrial propagation environment, and may even lead to microsecond-level propagation delay fluctuation, seriously affecting the timing accuracy of the system. Aiming at this problem, this paper proposes a propagation delay prediction model based on a Back-Propagation neural network (BPNN) for a complex meteorological environment, which realizes the function of directly mapping propagation delay fluctuation through meteorological factors. First, the theoretical influence of meteorological factors on each component of propagation delay is analyzed based on calculation parameters. Then, through the correlation analysis of the measured data, the complex relationship between the seven main meteorological factors and the propagation delay, as well as their regional differences, are demonstrated. Finally, a BPNN prediction model considering regional changes of multiple meteorological factors is proposed, and the validity of the model is verified by long-term collected data. Experimental results show that the proposed model can effectively predict the propagation delay fluctuation in the next few days, and its overall performance is significantly improved compared with that of the existing linear model and simple neural network model.