The invention belongs to the field of image analysis, and discloses an automatic classification method and system for pathological diagrams of cell and regional hierarchies, and the method comprises the following steps: (1) cutting an initial pathological diagram into small diagrams, and drawing a cell mask diagram; (2) carrying out image segmentation on the small image to obtain cell coordinates; (3) cutting the initial pathological map into single cell small maps, and judging cell types; (4) cutting the initial pathological diagram into small diagrams, and judging whether the small diagrams belong to a cancerous region and a para-cancerous region or not; (5) cutting the initial pathological diagram into small diagrams, and respectively judging whether the small diagrams belong to a tumor tissue parenchyma region, a mesenchymal region, a protein keratinization region and a vessel region or not; (6) integrating the scores, and determining the cell type and the belonging region thereof. According to the method, the overall process processing of the method is improved, so that the defect that the analysis of the pathological diagram stays in block type analysis in the prior art can be overcome, the information of the pathological diagram is deeply mined, and therefore, the automatic classification of the pathological diagram is realized.