Aimed at mitigating the limitations of the existing document entity relation extraction methods, especially the complex information interaction between different entities in the document and the poor effect of entity relation classification, according to the semi-structured characteristics of patent document data, a patent document ontology model construction method based on hierarchical clustering and association rules was proposed to describe the entities and their relations in the patent document, dubbed as MPreA. Combined with statistical learning and deep learning algorithms, the pre-trained model of the attention mechanism was fused to realize the effective extraction of entity relations. The results of the numerical simulation show that, compared with the traditional methods, our proposed method has achieved significant improvement in solving the problem of insufficient contextual information, and provides a more effective solution for patent document entity relation extraction.