Existing studies often lack a systematic solution for an Unmanned Aerial Vehicles (UAV) inspection system, which hinders their widespread application in crack detection. To enhance its substantial practicality, this study proposes a formal and systematic framework for UAV inspection systems, specifically designed for automatic crack detection and pavement distress evaluation. The framework integrates UAV data acquisition, deep-learning-based crack identification, and road damage assessment in a comprehensive and orderly manner. Firstly, a flight control strategy is presented, and road crack data are collected using DJI Mini 2 UAV imagery, establishing high-quality UAV crack image datasets with ground truth information. Secondly, a validation and comparison study is conducted to enhance the automatic crack detection capability and provide an appropriate deployment scheme for UAV inspection systems. This study develops automatic crack detection models based on mainstream deep learning algorithms (namely, Faster-RCNN, YOLOv5s, YOLOv7-tiny, and YOLOv8s) in urban road scenarios. The results demonstrate that the Faster-RCNN algorithm achieves the highest accuracy and is suitable for the online data collection of UAV and offline inspection at work stations. Meanwhile, the YOLO models, while slightly lower in accuracy, are the fastest algorithms and are suitable for the lightweight deployment of UAV with online collection and real-time inspection. Quantitative measurement methods for road cracks are presented to assess road damage, which will enhance the application of UAV inspection systems and provide factual evidence for the maintenance decisions made by road authorities.