The invention discloses a multifunctional flexible protective film with a gradient structure, relates to the field of electronic device protection in space environments and in particular relates to anano-film protective metal film flexible polymer functional protective material with a multilayer gradient structure, space charged particle radiation resistance and excellent electric and heat conductivity. The multifunctional flexible protective film aims at solving the problem that an existing space radiation protective material is large in weight, non-flexible, high in cost and easy to generate secondary particles. The multifunctional flexible protective film with the gradient structure is of a three-layer structure respectively comprising a nanotube film, a micro-nano elementary substancelayer and a flexible polymer; the nanotube film is a graphene film, a boron nitride nanotube or a carbon nanotube film; the elementary substance in the micro-nano elementary substance layer is aluminum, nickel, titanium, copper or silver; and the flexible polymer is low-density polyethylene, high-density polyethylene, ultra-high molecular weight polyethylene or a micro-nano particle doped polymer. The multifunctional flexible protective film with the gradient structure is used for protecting electronic devices.