Disclosed is a three-dimensional low-dose PET reconstruction method based on deep learning. The method comprises the following steps: back projecting low-dose PET raw data to the image domain to maintain enough information from the raw data; selecting an appropriate three-dimensional deep neural network structure to fit the mapping between the back projection of the low-dose PET and a standard-dose PET image; after learning from the training samples the network parameters are fixed, realizing three-dimensional PET image reconstruction starting from low-dose PET raw data, thereby obtaining a low-dose PET reconstructed image which has a lower noise and a higher resolution compared with the traditional reconstruction algorithm and image domain noise reduction processing.