Obstructive sleep apnea (OSA) syndrome is a common sleep disorder and a key cause of cardiovascular and cerebrovascular diseases that seriously affect the lives and health of people. The development of Internet of Medical Things (IoMT) has enabled the remote diagnosis of OSA. The physiological signals of human sleep are sent to the cloud or medical facilities through Internet of Things, after which diagnostic models are employed for OSA detection. In order to improve the detection accuracy of OSA, in this study, a novel OSA detection system based on manually generated features and utilizing a parallel heterogeneous deep learning model in the context of IoMT is proposed, and the accuracy of the proposed diagnostic model is investigated. The OSA recognition scheme used in our model is based on short-term heart rate variability (HRV) signals extracted from ECG signals. First, the HRV signals and the linear and nonlinear features of HRV are combined into a one-dimensional (1-D) sequence. Simultaneously, a two-dimensional (2-D) HRV time-frequency spectrum image is obtained. The 1-D data sequences and 2-D images are coded in different branches of the proposed deep learning network for OSA diagnosis. To validate the performance of the proposed scheme, the Physionet Apnea-ECG public database is used. The proposed scheme outperforms the existing methods in terms of accuracy and provides a novel direction for OSA recognition.