AbstractThe urban flow wind field is a critical element for downstream research, such as mitigation of urban wind disasters, assessment of urban wind environment, and urban drone route planning. However, it is impractical to arrange a large number of sensors to monitor an urban wind flow field. Hence, acquiring the entire urban wind flow field via sparse sensors would be highly valuable. To date, no scheme including deep learning (DL) model has been specifically designed for this purpose. This study presents an innovative approach to reconstruct complex high‐resolution urban wind fields based on sparse sensors, using a physics‐informed graph neural network (GNN)‐assisted auto‐encoder. The proposed method leverages the relationship between sensors and their surrounding environment enabled by deep mining capabilities of GNNs. As a result, the utilization and emphasis on sparse sensors data are significantly enhanced. The continuity equation of fluid flow is incorporated into the loss function of the convolution neural network to improve the stability and performance of the model. The findings suggest that, in contrast to prevalent generative DL models, the proposed model yields an approximate 50% reduction in root mean square error for reconstructing high‐resolution urban wind fields for multiple wind attack angles.