Background: Estimating the depth of anaesthesia (DoA) is critical in modern anaesthetic practice. Multiple DoA monitors based on electroencephalograms (EEGs) have been widely used for DoA monitoring; however, these monitors may be inaccurate under certain conditions. In this work, the hypothesis that heart rate variability (HRV)-derived features based on a deep neural network can distinguish different anaesthesia states was investigated.Methods: A novel method of distinguishing different anaesthesia states was developed based on four HRV-derived time and frequency domain features combined with a deep neural network. Four features were extracted from an electrocardiogram, including the HRV high-frequency power, low-frequency power, high-to-low-frequency power ratio, and sample entropy. Next, these features were used as inputs for the deep neural network, which used the expert assessment of consciousness level as the reference output. Finally, the deep neural network was compared with the logistic regression, support vector machine, and decision tree models. The datasets of 23 anaesthesia patients were used to assess the proposed method.Results: The accuracies of the four models, in distinguishing the anaesthesia states, were 86.2% (logistic regression), 87.5% (support vector machine), 87.2% (decision tree), and 90.1% (deep neural network). The accuracy of deep neural network was higher than those of the logistic regression (p < 0.05), support vector machine (p < 0.05), and decision tree (p < 0.05) approaches. Our method outperformed the logistic regression, support vector machine, and decision tree methods.Conclusions: The incorporation of four HRV-derived time and frequency domain features and a deep neural network could accurately distinguish between different anaesthesia states; however, this study is a pilot of a feasibility study, providing a method to supplement DoA monitoring based on EEG features to improve the accuracy of DoA estimation.