The invention provides a filter element which has a reduced initial pressure loss, can reduce an energy cost and can secure a high air flow rate, a filter element which has an elongated gas removing service life and filtering service life while keeping a high gas removing performance and a high dust removing efficiency, a manufacturing method and a method of use of the same. In a filter element (10) in which a pleated composite substrate (11) obtained by lapping or laminating an nonwoven fabric sheet including a fiber constituted by a thermoplastic resin and a gas removal sheet is pleated, and a pleated shape of the pleated composite substrate (11) is held by a shape retaining member (12a), a thickness of the nonwoven fabric sheet is increased at least 5% when heated to 60 degree C.