Marine fouling organisms are very harmful to the immersed surface of the ship hull. The antifouling technology based on surface microstructure is a green antifouling method that will not cause any harm to the marine ecological environment, so it has been studied emphasically in recent years. The work analyzed the surface microstructure characteristics of many self-cleaning animals and plants in nature and summarized the research progress of surface microstructure antifouling mechanism. Moreover, several existing antifouling theoretical models of microstructure were described: engineered roughness index model, engineered nanoforce gradients model and surface energetic attachment model. The methods to process micron-scale structures, nano-scale structures and micro-nano-composite structures were reviewed and the common evaluation methods for antifouling performance of microstructures were discussed: real ship test method, shallow sea submergence test method, contact angle test method, adhesion measurement test method and biological adhesion test method. Based on typical marine fouling organisms such as bacteria, ulva spores, diatoms and barnacle larvae, the antifouling properties of surface microstructures were analyzed. Then, the further studying of the adhesion mechanism of marine fouling organisms and antifouling mechanism of surface microstructure is proposed to establish surface microstructure design benchmark. The rapid and accurate processing of multi-scale micro/nano structure and the perfecting evaluation system of antifouling performance are the key problems and future directions in the development of surface microstructure antifouling technologies.