Unmanned aerial vehicles (UAV) and related technologies have played an active role in the prevention and control of novel coronaviruses at home and abroad, especially in epidemic prevention, surveillance, and elimination. However, the existing UAVs have a single function, limited processing capacity, and poor interaction. To overcome these shortcomings, we designed an intelligent anti-epidemic patrol detection and warning flight system, which integrates UAV autonomous navigation, deep learning, intelligent voice, and other technologies. Based on the convolution neural network and deep learning technology, the system possesses a crowd density detection method and a face mask detection method, which can detect the position of dense crowds. Intelligent voice alarm technology was used to achieve an intelligent alarm system for abnormal situations, such as crowd-gathering areas and people without masks, and to carry out intelligent dissemination of epidemic prevention policies, which provides a powerful technical means for epidemic prevention and delaying their spread. To verify the superiority and feasibility of the system, high-precision online analysis was carried out for the crowd in the inspection area, and pedestrians’ faces were detected on the ground to identify whether they were wearing a mask. The experimental results show that the mean absolute error (MAE) of the crowd density detection was less than 8.4, and the mean average precision (mAP) of face mask detection was 61.42%. The system can provide convenient and accurate evaluation information for decision-makers and meets the requirements of real-time and accurate detection.