In this research, an innovative 3D micromachining process for functional microstructures on curved surfaces is introduced. An injection molded 3D polymethylmethacrylate (PMMA) microlens array was used as projection optics. A layer of positive photoresist SPR 220 was spin coated on a curved substrate. Preselected patterns were projected onto the photoresist by using a home-built exposure system. Microstructures were created on the curved substrate after development. The 3D projection micromachining method was evaluated through several experiments, and predesigned masks were prepared to fabricate microstructure array of various dimensions and distributions, demonstrating its 3D micromachining capabilities. Finally, this method was utilized to control the surface roughness of the curved substrates by generating microsquare protuberance arrays, forming a 3D functionally graded material (FGM). Further experimental results using a goniometer showed that this method can create functional microstructures for wettability control on steep curved substrates. All these results indicated that the proposed micromachining process is capable of fabricating 3D microstructures on curved surfaces and provides a cost-effective solution to challenging manufacturing problems.