Abstract In order to study the security of Internet of drones (IoD), convolutional neural network (CNN) algorithm was compared with autonomous IoD. Moreover, wireless communication technology was used to analyze and design a more optimized model for system security performance. The model constructed was simulated, and relevant data were collected to verify its security performance. The results show that the clustering algorithm based on node energy has the best performance in the performance analysis of IoD. When the number of nodes is appropriate, it can avoid wasting bandwidth resources and overloading, and the number of switching between clusters is less than other algorithms. Therefore, EWCA algorithm can be used to improve the lifetime of the whole network and enhances the availability of IoD. When analyzing the security performance based on the system security interruption probability, it is found that the lower the security interruption rate is when the energy acquisition coefficient α is close to 0.5, the longer the IoD is used for information transmission, and the better the security performance is. The greater the signal-to-noise ratio is, the better the network security performance is, and the network performance is the best when the number of nodes tends to be 10. Therefore, through the research, it is found that the model built increases the security of IoD. Although there are some shortcomings in the experimental process, it still provides experimental basis for the later development of IoD.