The limited throughput of nano-scale laser lithography has been the bottleneck for its industrial applications. Although using multiple laser foci to parallelize the lithography process is an effective and straightforward strategy to improve rate, most conventional multi-focus methods are plagued by non-uniform laser intensity distribution due to the lack of individual control for each focus, which greatly hinders the nano-scale precision. In this paper, we present a highly uniform parallel two-photon lithography method based on a digital mirror device (DMD) and microlens array (MLA), which allows the generation of thousands of femtosecond (fs) laser foci with individual on-off switching and intensity-tuning capability. In the experiments, we generated a 1,600-laser focus array for parallel fabrication. Notably, the intensity uniformity of the focus array reached 97.7%, where the intensity-tuning precision for each focus reached 0.83%. A uniform dot array structure was fabricated to demonstrate parallel fabrication of sub-diffraction limit features, i.e., below 1/4 λ or 200 nm. The multi-focus lithography method has the potential of realizing rapid fabrication of sub-diffraction, arbitrarily complex, and large-scale 3D structures with three orders of magnitude higher fabrication rate.