Aiming at the problems that the intrusion detection methods of Internet of Medical Things (IoMT) rely on the balance of data samples, the misuse detection based on supervised learning cannot cope with unknown attacks, and the false alarm rate of anomaly detection based on unsupervised learning is high, an intrusion detection method with multi-stage fusion for IoMT was proposed. Firstly, a feature extraction method that added header information and payload to the bidirectional flow features was adopted to reduce the dependence on the balance of data samples. Then, a three-stage intrusion detection framework was designed by combining supervised and unsupervised learning methods. In the framework, the unsupervised learning AutoEncoder (AE) model was used to filter benign traffic and detect unknown attacks, and the supervised learning hybrid model of Convolutional Neural Network (CNN), Gated Recurrent Unit (GRU), and Attention mechanism (Attention) was used to detect known attacks and reduce false alarms, so as to improve the detection performance. Experimental results show that Multi-stage fusion for IoMT Intrusion Detection System (MTIDS) constructed by the proposed method achieves 99.96% detection accuracy and 93.78% F1 value on the CICIoMT2024 and CICIoT2023 datasets, which are higher than those of intrusion detection models of single supervised or unsupervised learning methods such as AE. Specifically, MTIDS has an improvement of 0.82 percentage points in accuracy and 5.58 percentage points in F1 value compared to the best comparison model AE, which validates the accuracy of the proposed method in detecting known and unknown attacks.