The invention discloses low surface energy polymer microcapsules and a preparation method thereof, and relates to the field of coating industry. The microcapsules consist of a low surface energy polymer core material and a wall material prepolymer, wherein the low surface energy polymer core material is a fluorine silicon polymer, an organic silicon polymer or a fluorocarbon polymer; the wall material prepolymer is a water-soluble urea resin prepolymer; and the mass ratio of the low surface energy polymer to the wall material prepolymer is (40-60): (45-80). The preparation method comprises the following steps of: preparing water dispersion of the low surface energy polymer core material according to the formula, preparing the water-soluble urea resin prepolymer serving as the wall material according to the formula, dripping and dispersing the water-soluble urea resin prepolymer into the water dispersion of the low surface energy polymer core material, and obtaining the low surface energy polymer microcapsules by heating reaction. The wall material and the coating resin base material have excellent compatibility, the low surface energy core material is released and dispersed in thecoating to endow the coating with excellent low surface energy property, and the low surface energy core material is widely suitable for preparing various low surface energy antifouling coatings and flow resistance reducing coatings.