Polyisoprene is widely used in the industrial production of tires, thermoplastic elastomers, pressure sensitive adhesives, coatings, plasticizers, lubricants, and other functional materials. However, due to the inherent molecular defect of containing many unsaturated double bonds, polyisoprene exhibits relatively weak environmental endurance, especially under extreme environmental conditions. To incorporate the excellent features of fluorinated polymer such as tough environmental endurance, a new type of fluorinated polyisoprene is tailored and a facile procedure of introducing fluoroalkyl side chains onto polyisoprene backbone is carried out via epoxidation and thiol–epoxy click chemistry under mild conditions. The results demonstrate that fluorinated alkyl side chains are successfully clicked onto backbone chains of polyisoprene and the corresponding film exhibits a microphase separation structure. As for the fluorinated polyisoprene film after the introduction of fluoroalkyl groups, the water contact angle enhances significantly from 79.4° to 114.8° and the UV reflectivity improves markedly. In addition, the surface chemical constituents confirm that the incorporated fluoroalkyl groups have a tendency to migrate and enrich spontaneously onto the film surface.