The invention provides an intelligent encoding method and system of Chinese disease diagnoses based on a word segmentation network. The method includes following steps: step 1, obtaining a Chinese disease diagnosis name; step 2, matching the Chinese disease diagnosis name with a dynamic extended word segmentation network, extracting key information from the Chinese disease diagnosis name, and forming a key word group through the extracted key information; and step 3, matching the key word group with a word group encoding mapping table and outputting an unmatched result or an ICD code. Comparedwith the prior art, the beneficial effects of the method and system are that firstly, standard encoding of medical record data in a heterogeneous condition is unified, a solid data standardization support is provided for management and decision of the medical quality and the medical health insurance fund, and gradual standardization and normalization of our national clinical medical practice arepromoted; secondly, the encoding operation of the ICD can be automatically accomplished, manual participation is avoided, the encoding speed is high, the cost is low, and the accuracy is high; and thirdly, unified and standard ICD codes can be achieved.