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In this paper, a data-driven framework aimed at investigating how weather factors affect the spatio-temporal patterns of air traffic flow in the terminal maneuvering area (TMA) is presented. The framework mainly consists of three core modules, namely, trajectory structure characterization, flow pattern recognition, and association rule mining. To fully characterize trajectory structure, abnormal trajectories and typical operations are sequentially extracted based on a deep autoencoder network with two specially designed loss functions. Then, using these extracted elements as basic components to further construct and cluster per-hour-level descriptions of airspace structure, the spatio-temporal patterns of air traffic flow can be recognized. Finally, the association rule mining technique is applied to find sets of weather factors that often appear together with each flow pattern. Experimental analysis is demonstrated on two months of arrival flight trajectories at Hong Kong International Airport (HKIA). The results clearly show that the proposed framework effectively captures spatial anomalies, fine-grained trajectory structures, and representative flow patterns. More importantly, it also reveals that those flow patterns with non-conforming behaviors result from complex interactions of various weather factors. The findings provide valuable insights into the causal relationships between weather factors and changes in flow patterns, greatly enhancing the situational awareness of TMA.