In order to automatically identify thyroid lymph node metastases, a deep leaning pathology diagnosis of multitask centers was proposed. The structure observation task center under the microscope and the cell observation task center under the microscope were constructed based on the convolution neural network algorithm, which used to simulate the complete diagnosis process, and the observation factors of center are various. The intuitionistic fuzzy set was used to give the comprehensive diagnosis results.SThe method simulates the whole diagnostic process of doctors, the experimental result shows that the method is effective and the recognition rate of thyroid lymph node metastases is satisfactory.