Computational fluid dynamics (CFD) simulation is a core component of wind engineering assessment for urban planning and architecture. CFD simulations require clean and low-complexity models. Existing modeling methods rely on static data from geographic information systems along with manual efforts. They are extraordinarily time-consuming and have difficulties accurately incorporating the up-to-date information of a target area into the flow model. This paper proposes an automated simulation framework with superior modeling efficiency and accuracy. The framework adopts aerial point clouds and an integrated two-dimensional and three-dimensional (3D) deep learning technique, with four operational modules: data acquisition and preprocessing, point cloud segmentation based on deep learning, geometric 3D reconstruction, and CFD simulation. The advantages of the framework are demonstrated through a case study of a local area in Shenzhen, China.