Machine learning techniques are being widely used to develop an intrusion detection system (IDS) for detecting and classifying cyber attacks at the network-level and the host-level in a timely and automatic manner. However, Traditional Intrusion Detection Systems (IDS), based on traditional machine learning methods, lacks reliability and accuracy. Instead of the traditional machine learning used in previous researches, we think deep learning has the potential to perform better in extracting features of massive data considering the massive cyber traffic in real life. Generally Mobile Ad Hoc Networks have given the low physical security for mobile devices, because of the properties such as node mobility, lack of centralized management and limited bandwidth. To tackle these security issues, traditional cryptography schemes can-not completely safeguard MANETs in terms of novel threats and vulnerabilities, thus by applying Deep learning methods techniques in IDS are capable of adapting the dynamic environments of MANETs and enables the system to make decisions on intrusion while continuing to learn about their mobile environment. An IDS in MANET is a sensoring mechanism that monitors nodes and network activities in order to detect malicious actions and malicious attempt performed by Intruders. Recently, multiple deep learning approaches have been proposed to enhance the performance of intrusion detection system. In this paper, we made a systematic comparison of three models, Inceprtion architecture convolutional neural network Inception-CNN, Bidirectional long short-term memory (BLSTM) and deep belief network (DBN) on the deep learning-based intrusion detection systems, using the NSL-KDD dataset containing information about intrusion and regular network connections, the goal is to provide basic guidance on the choice of deep learning methods in MANET.