This paper exploits multi-modal Physical (PHY)-layer features in terms of artificial fingerprint, In-phase/Quadrature (IQ) imbalance and Angle of Arrival (AoA) to propose a novel PHY-layer authentication framework for a Millimeter Wave (mmWave) Multiple-Input Multiple-Output (MIMO) Unmanned Aerial Vehicle (UAV)-enabled communication system. First, we resort to the AoA-based spatial fingerprint to effectively address the challenge of channel fingerprint instability induced by high-speed UAV mobility. To further enhance the low discriminability of hardware fingerprints caused by refined manufacturing techniques, artificial Gaussian noise is injected into the transmission signals to assist the receiver in better distinguishing between legitimate and illegitimate UAVs. Then, we jointly combine with inherent IQ imbalance and AoA features to design a hybrid authentication scheme and thus construct a multi-dimensional fingerprint space for a comprehensive characterization of UAV identities. To theoretically evaluate the effectiveness of the proposed authentication framework, the analytical closed-form expressions of performance metrics like false alarm and detection probabilities are also exactly derived based on the statistical signal processing technology and composite hypothesis testing. Finally, we provide large simulation results to validate the correctness and feasibility of the proposed theoretical models, and also discuss the relation between system security and communication service quality under different artificial fingerprint level.