Super-hydrophilic and oleophobic functional materials can prevent pollution or adsorption by repelling oil, and have good circulation. However, traditional strategies for preparing these functional materials either use expensive fabrication machines or contain possibly toxic organic polymers, which may prohibit the practical application. The research of multifunctional ZnO microstructures or nanoarrays thin films with super-hydrophilic, antifouling, and antibacterial properties has not been reported yet. Moreover, the exploration of underwater oleophobic and self-cleaning antifouling properties in ZnO micro/nanostructures is still in its infancy. Here, we prepared ZnO microstructured films on fluorine-doped tin oxide substrates (F-ZMF) for the development of advanced self-cleaning type super-hydrophilic and oleophobic materials. With the increase of the accelerators, the average size of the F-ZMF microstructures decreased. The F-ZMF shows excellent self-cleaning performance and hydrophilic (water contact angle ≤ 10°) and oleophobic characteristics in the underwater antifouling experiment. Under a dark condition, F-ZMF-4 showed good antibacterial effects against () and () with inhibition rates of 99.1% and 99.9%, respectively. This study broadens the application scope of ZnO-based material and provides a novel prospect for the development of self-cleaning super-hydrophilic and oleophobic materials.