In this paper, we investigate tags in anti-collision applications of radio frequency identification (RFID) technology in unmanned aerial vehicle (UAV)-aided vehicular ad hoc networks (VANETs). The integration of RFID technology in UAV-aided VANETs can provide reliable traffic-related services for vehicles. However, multiple tags’ simultaneous responses to a reader mounted on a UAV, denoted as tag collision, gravely affect the correct tag detection on each vehicle. Therefore, in order to decrease the collision probability and improve the throughput, we propose a multi-frequency tag identification method. In the proposed scheme, we devise a tag grouping method based on adaptive power control to make the reader dynamically match the optimal frame length. Based on the above matching results, we introduce a tag estimation method using the optimal weight to improve the accuracy of tag estimation. We theoretically analyze the closed-form expression of the security outage probability expression. Finally, our simulation results demonstrate that the proposed tag anti-collision scheme achieved significant performance superiority in terms of the throughput and identification time slots.