Traffic scene understanding from unmanned aerial vehicle (UAV) platforms is crucial for intelligent transportation systems due to its flexible deployment and wide-area monitoring capabilities. However, existing methods face significant challenges in real-world surveillance, as their heavy reliance on optical imagery leads to severe performance degradation under adverse illumination conditions like nighttime and fog. Furthermore, current Visual Question Answering (VQA) models are restricted to elementary perception tasks, lacking the domain-specific regulatory knowledge required to assess complex traffic behaviors. To address these limitations, we propose a novel Multi-modal Traffic Cognition Network (MTCNet) for robust UAV traffic scene understanding. Specifically, we design a Prototype-Guided Knowledge Embedding (PGKE) module that leverages high-level semantic prototypes from an external Traffic Regulation Memory (TRM) to anchor domain-specific knowledge into visual representations, enabling the model to comprehend complex behaviors and distinguish fine-grained traffic violations. Moreover, we develop a Quality-Aware Spectral Compensation (QASC) module that exploits the complementary characteristics of optical and thermal modalities to perform bidirectional context exchange, effectively compensating for degraded features to ensure robust representation in complex environments. In addition, we construct Traffic-VQA, the first large-scale optical-thermal infrared benchmark for cognitive UAV traffic understanding, comprising 8,180 aligned image pairs and 1.3 million question-answer pairs across 31 diverse types. Extensive experiments demonstrate that MTCNet significantly outperforms state-of-the-art methods in both cognition and perception scenarios. The dataset is available at https://github.com/YuZhang-2004/UAV-traffic-scene-understanding.