Physical unclonable function (PUF) has emerged as a unique physical'fingerprint' that is inherently difficult to replicate. It shows tremendous application value in various hardware security areas such as identity authentication, chip anticounterfeiting, communication encryption, blockchain, etc. However, with the rapid development of 3D nanoprinting, classical PUFs constructed with disordered micro‐nanostructures face tremendous threats from physical cloning attacks. Herein, this study proposes and demonstrates the utilization of room‐temperature single‐photon emitters derived from atomic defects in randomly distributed pyramidal aluminum nitride (AlN) nanocrystals as a novel quantum PUF to resist physical cloning attacks. The fabrication of this quantum PUF on silicon (Si) wafers enables seamless integration with silicon photonic integrated circuits. The multidimensional fingerprint features of the single‐photon emitters are highly sensitive to the lattice parameters of the uneven AlN nanocrystals. Furthermore, each single photon emitter can work as a quantum random number generator to ensure the fundamental unpredictability of PUFs. The subatomic precision requirement coupled with unpredictable quantum emission behavior makes it practically impossible to attack the proposed quantum PUF, providing a promising solution for information security in the post‐quantum era.