For the fuzziness of the membership degree of fuzzy subsets, the concept of a type2 fuzzy set and the rationality of describing the reality with it are introduced. Beginning with the practical problems, the concept of generalized fuzzy soft sets is proposed. On that basis, the inclusion relation, intersection, union, complement operations and related properties of generalized fuzzy soft sets are studied. Besides, this paper discusses fuzzy soft relation and fuzzy soft matrix based on generalized fuzzy soft sets, and further explores the operations and properties as generalized fuzzy soft sets. Finally, the generalized fuzzy soft sets are applied to medical diagnosis, a patient's type of his or her disease is judged by defuzzification and construction of score function, and the feasibility and validity of the generalized fuzzy soft set are verified.