A device’s intrinsic security fingerprint, representing its physical characteristics, serves as a unique identifier for user devices and is highly regarded in the realms of device security and identity recognition. However, fluctuations in the environmental noise can introduce variations in the physical features of the device. To address this issue, this paper proposes an innovative method to enable the device’s intrinsic security fingerprint to adapt to environmental changes, aiming to improve the accuracy of the device’s intrinsic security fingerprint recognition in real-world physical environments. This paper initiates continuous data collection of device features in authentic noisy environments, recording the temporal changes in the device’s physical characteristics. The problem of unstable physical features is framed as a restricted statistical learning problem with a localized information structure. This paper employs an aggregated hypergraph neural network architecture to process the temporally changing physical features. This allows the system to acquire aggregated local state information from the interactive influences of adjacent sequential signals, forming an adaptive environment-enhanced device intrinsic security fingerprint recognition model. The proposed method enhances the accuracy and reliability of device intrinsic security fingerprint recognition in outdoor environments, thereby strengthening the overall security of terminal devices. Experimental results indicate that the method achieves a recognition accuracy of 98% in continuously changing environmental conditions, representing a crucial step in reinforcing the security of Internet of Things (IoT) devices when confronted with real-world challenges.