Flight delay serves as a pivotal metric for assessing service quality in the aviation industry. Accurately estimating flight delay duration is increasingly acknowledged as a cornerstone of aviation management, with significant implications for operational efficiency, passenger satisfaction, and economic outcomes. Most existing approaches often focus on single airports or airlines and overlook the complex interdependencies within the broader aviation network, limiting their applicability for system-wide planning. To address this gap, this study proposes a novel integrated framework that combines deep learning and complex network theory to predict flight arrival delay duration from a multi-airport and multi-airline perspective. Leveraging Bayesian optimization, we fine tune hyperparameters in the XGBoost algorithm to extract critical aviation network features at both node (airports) and edge (flight routes) levels. These features, which capture structural properties such as airport congestion and route criticality, are then used as inputs for a deep kernel extreme learning machine to estimate delay duration. Numerical experiment using a high-dimensional flight dataset from the U.S. Bureau of Transportation Statistics reveals that the proposed framework achieves superior accuracy, with an average delay error of 3.36 min and a 7.8% improvement over established benchmark methods. This approach fills gaps in network-level delay prediction, and the findings of this research could provide valuable insights for the aviation administration, aiding in making informed decisions on proactive measures that contribute to the sustainable development of the aviation industry.