Based on strong isomorphism for hypergraphs,vertex isomorphism is defined,which preserves hyper-adjacency property between vertices.Adjacency-matrixes of hypergraphs and weighted hypergraphs are presented respectively.The Floyd's algorithm is generalized to finding shortest paths between all pairs of vertices in a hypergraph.The publication provides an instance which verifies the practicability of the modified algorithm and whose results have been compared with those of the method given by LI Chun-ming.Time complexity of the presented algorithm is obtained to be(O(n~3)).