The invention discloses a matching method of semantic WEB service and a system thereof. Based on similarity between request and candidate service, the matching method and the system synthetically consider functional and non-functional factors, and introduce a phasing filtering mechanism. The matching method and the system adopt single-concept semantic matching algorithm, take depth, inheritance relation and binary relation into full account so that a body relationship structure is formed into a graphic structure rather than a tree-shaped structure, and the multiple inheritance problems and loop problems are processed during calculation of semantic distance based on the graph. The adopted multi-concept semantic matching algorithm has introduced a processing of repeated matching. During input and output matching, the number of parameters are taken into account, a method for calculating similarity in three levels is adopted, therefore,, the matching is more efficient; and the matching method and the system also takes into account factors of user preferences and service quality, therefore, the precision of matching and efficiency of response can be further improved.