Aiming at the accuracy of patent value evaluation in bio-pharmaceutical industry, combining industrial technology factors and patent characteristics, the patent value evaluation index system and its industrial patent value evaluation model were constructed to reflect the characteristics of industry individuality. The auto encoder (AE) was used to reduce the dimension of the original patent information, and then the patent value evaluation model was established based on the spectral clustering algorithm (SC), and the support vector machine (SVM) was used to classify the patent information, so as to verify the validity of the model. The results show that the model can effectively reflect the level of patent value, and effectively verify that relevant information such as patent years, drug patent types and indications are necessary factors to consider in the evaluation of bio-pharmaceutical industry technology patents. This study provides a new perspective and method for the evaluation of industrial patent value.