In recent years, although the application of knowledge graph in natural language processing has made some progress, there are still some key problems to be solved, especially the matching query problem in natural language knowledge graph. Since the basic data model of knowledge graph is graph, the matching query problem in natural language knowledge graph is usually transformed into graph matching query problem. However, at present, the traditional graph matching technology applied in knowledge graph consumes too much time and has low query efficiency, which cannot meet the needs of users for large-scale natural language knowledge graph query. Based on the full analysis of the defects of the traditional graph matching technology applied in the knowledge graph, according to the characteristics of the natural language knowledge graph, in order to improve the query efficiency, we propose an accurate matching query method of graph hierarchical topological sequence based on the graph model of knowledge graph. Through experiment analysis, compared with the traditional graph model matching algorithm applied in knowledge graph query, this method can quickly filter the unqualified knowledge graph candidate sets, effectively reduce the number of knowledge graph candidate sets, and make it have more advantages in matching efficiency and time performance. In addition, compared with two algorithms of GIndex and FG-Index, this method has better performance in index construction time, average size of candidate set and average running time of online update.