The invention provides an infant brain magnetic resonance image partitioning method based on a fully convolutional network. The main content of the method comprises the multi-stream three-dimensionalfully convolutional network (FCN) with jump connection, partial transfer learning, training and testing and evaluation. According to the process of the method, first, a probability graph of each pieceof brain tissue is learned from a multi-modal magnetic resonance image; second, initial partitions of different brain tissue are obtained from the probability graphs and used for calculating a distance graph of each piece of brain tissue; third, spatial context information is simulated according to the distance graphs; and last, final partitioning is realized by use of spatial correlation information and the multi-modal magnetic resonance image, wherein the training process mainly comprises training data increasing, training patch preparation and iterative training, and various detection values are used for evaluation after testing is performed. Through the partitioning method, a white matter area, a grey matter area and a cerebrospinal fluid area are successfully divided, the potential gradient vanishing problem of multi-level deep supervision is relieved, training efficiency is improved, and partitioning performance is greatly enhanced.