The invention discloses a preparation method of a flexible anti-drag skin of a micro-electromechanical system (MEMS). The method comprises the following steps: providing a substrate; forming a flexible substrate on the base; preparing a patterned electrode on the flexible substrate, wherein the patterned electrode comprises a plurality of electrolytic anodes and electrolytic cathodes, which are arranged in a staggered manner; preparing micro convex column arrays on the flexible substrate and the patterned electrode by using a photoresist; filling first pre-polymer into a convex column gap of the micro convex column arrays; solidifying the first pre-polymer after the first pre-polymer is filled; polymerizing into a first polymer from the first pre-polymer, so as to obtain a flexible surface layer; removing the micro convex column arrays by using an etching technology, so that the patterned electrode at the bottom of the convex column is exposed, and meanwhile, a micro-concave pit array is formed; stripping the base, so as to obtain the flexible anti-drag skin of the MEMS.