Currently, deep learning aided medical imaging is becoming the hot spot of AI frontier application and the future development trend of precision neuroscience. This review aimed to render comprehensive and informative insights into the recent progress of deep learning and its applications in medical imaging for brain monitoring and regulation. The article starts by providing an overview of the current methods for brain imaging, highlighting their limitations and introducing the potential benefits of using deep learning techniques to overcome these limitations. Then, we further delve into the details of deep learning, explaining the basic concepts and providing examples of how it can be used in medical imaging. One of the key strengths is its thorough discussion of the different types of deep learning models that can be used in medical imaging including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and generative adversarial network (GAN) assisted magnetic resonance imaging (MRI), positron emission tomography (PET)/computed tomography (CT), electroencephalography (EEG)/magnetoencephalography (MEG), optical imaging, and other imaging modalities. Overall, our review on deep learning aided medical imaging for brain monitoring and regulation provides a referrable glance for the intersection of deep learning aided neuroimaging and brain regulation.