The fuzzy vault is an innovative way to share secret keys, combining traditional cryptography with biometrics and biometric template protection. This method forms the basis for the reliable operation of unmanned aerial vehicles (UAVs) through anonymizing drone operators and safely using their data and onboard information. However, due to the inherent instability of biometrics, traditional fuzzy vault schemes face challenges, such as reduced recognition rates with increased chaff points, impractical runtimes due to high-order polynomial reconstruction, and susceptibility to correlation attacks. This paper proposes an efficient fuzzy vault scheme to address these challenges. We generate two secret keys based on biometrics: the first key is produced from the operator’s unique features like the face and iris, using a confidence interval; the second key, used to construct a polynomial, is based on what the operator remembers. These dual-key fuzzy vaults enable the stable generation of genuine points during encoding, easy extraction during decoding, and effective operator authentication while maintaining anonymity. Our experimental results demonstrate improved security and secret acquisition accuracy using the AR face database. These results are achieved regardless of increased false vaults, enabling real-time polynomial reconstruction and resilience against correlation attacks. Importantly, our enhanced fuzzy vault scheme allows the application of this secure, real-time authentication process, safeguarding the anonymity of drone operators.