A flexible and efficient strategy, digital micromirror devices (DMD) based multistep lithography (DMSL), is proposed to fabricate arrays of user-defined microstructures. Through the combination of dose modulation, flexible pattern generation of DMD, and high-resolution step movement of piezoelectrical stage (PZS), this method enables prototyping a board range of 2D lattices with periodic/nonperiodic spatial distribution and arbitrary shapes and the critical feature size is down to 600 nm. We further explore the use of DMSL to fabricate microlens array by combining with the thermal reflowing process. The square shape and hexagonal shape microlens with customized distribution are realized and characterized. The results indicate that the proposed DMSL can be a significant role in the microfabrication techniques for manufacturing functional microstructures array.