It is difficult for the current spatial knowledge representation model based on general graph theory to reflect the complex composition and the implying organizational structure of the knowledge system. To cope with the above problem, this paper proposes a spatial knowledge representation model based on hybrid hypergraph, which is utilized to represent the spatial knowledge network with large scales, complicated connections and nested characteristics. The proposed model uses the hyperedges in the hybrid hypergraph to express multi element spatial relationship. Moreover, this paper also extends the topological relations in the basic dual element regions, and utilizes the topological relations in the multi element regions to qualitatively describe such relationships as separation, connection, and inclusion. Finally, presentation of one simple environment is taken as an example to illustrate the application of the spatial knowledge model based on hybrid hypergraph, which provide a new tool and approach to the expression, organization and analysis of complex spatial knowledge representation.