An automatic ship tracking method and system based on deep learning network and mean shift, wherein the method includes: collecting surveillance video data which includes collecting coastal region surveillance video data under visible light and extracting each frame of image; performing preprocessing to extract a positive sample and a negative sample of a ship target; inputting the samples of the ship target in the video into a neural network to train a model by a region-based convolutional neural network method; extracting initial frame data of the video and performing ship detection and probability density calculation on initial moment data according to the trained model; and determining a ship tracking result at the current moment by a calculation result of a previous moment.