A method for analysing medical treatment data based on deep learning via an intelligent analyser thereof, effectively alleviates work stress for doctors in a hospital or medical researchers and performs scientific analysis on a large amount of medical treatment data or medical data and obtain an analysis result matched therewith. The core content of the method is the establishment of a model in a computer using a deep convolution neuron algorithm in deep learning. The model assists the doctors to make correct judgments and effective decisions for the large amount of medical treatment data using mass medical treatment data selection and optimization model parameters by “training” the model to automatically learn a pathology analysis process of the doctors or the medical researchers and then helping them in processing the large amount of medical treatment data or medical data.