As air transportation demand continues to rise, congestion in air route networks has seriously compromised the safe and efficient operation of air traffic. Few studies have examined the spatiotemporal characteristics of congestion propagation under different time lag conditions. To address this gap, this study proposes a cross-segment congestion-propagation causal time-lag analysis framework. First, to account for the interdependency across segments in air route networks, we construct a point–line congestion state assessment model and introduce the FCM-WBO algorithm for precise congestion state identification. Next, the Multi-Channel Attention DSNG-BiLSTM model is designed to estimate the causal weights of congestion propagation between segments. Finally, based on these causal weights, two indicators—CPP and CPF—are derived to analyze the spatiotemporal characteristics of congestion propagation under various time lag levels. The results indicate that our method achieves over 90% accuracy in estimating causal weights. Moreover, the propagation features differ significantly in their spatiotemporal distributions under different time lags. Spatially, congestion sources tend to spread as time lag increases. We also identify segments that are likely to become overloaded, which serve as the primary receivers of congestion. Temporally, analysis of time-lag features reveals that because of higher traffic flow during peak periods, congestion propagates 36.92% more slowly than during the early-morning hours. By analyzing congestion propagation at multiple time lags, controllers can identify potential congestion sources in advance. They can then implement targeted interventions during critical periods, thereby alleviating congestion in real time and improving route-network efficiency and safety.