Most current representations of protein pockets are the atom-pair graph, which ignore the global structural information of amino acids. Therefore, we propose a new molecular generation model, which uses the hypergraph to represent protein pocket structure, and combines the structural features obtained by atom-pair graph representation. These two levels of graphs are more capable of representing the complex structural information of protein pockets. Then, the graphs of the two levels of the protein pockets are input into the improved network model, which is named Hypergraph Graph Attention Fusion (HGAF), to obtain the embedding representation of the protein pockets, which is used as a condition to constrain the molecule generation. The molecules sampled by HGAF are subjected to quality assessment and docking targeting validation. Experimental results show that the molecules generated by proposed method can achieve better results in both of these assessment approaches.