Drone developments, especially small-sized drones, usher in novel trends and possibilities in various domains. Drones offer navigational inter-location services with the involvement of the Internet of Things (IoT). On the other hand, drone networks are highly prone to privacy and security risks owing to their strategy flaws. In order to achieve the desired efficiency, it is essential to create a secure network. The purpose of the current study is to have an overview of the privacy and security problems that recently impacted the Internet of Drones (IoD). An Intrusion Detection System (IDS) is an effective approach to determine the presence of intrusions in the IoD environment. The current study focuses on the design of Crystal Structure Optimization with Deep-Autoencoder-based Intrusion Detection (CSODAE-ID) for a secure IoD environment. The aim of the presented CSODAE-ID model is to identify the occurrences of intrusions in IoD environment. In the proposed CSODAE-ID model, a new Modified Deer Hunting Optimization-based Feature Selection (MDHO-FS) technique is applied to choose the feature subsets. At the same time, the Autoencoder (AE) method is employed for the classification of intrusions in the IoD environment. The CSO algorithm, inspired by the formation of crystal structures based on the lattice points, is employed at last for the hyperparameter-tuning process. To validate the enhanced performance of the proposed CSODAE-ID model, multiple simulation analyses were performed and the outcomes were assessed under distinct aspects. The comparative study outcomes demonstrate the superiority of the proposed CSODAE-ID model over the existing techniques.