Fused-silica-based microlens array (MLA) has excellent stability in the harsh environment. However, it is still a challenge to efficiently prepare superhydrophobic quasi-periodic MLA and keep the optical performance of the microlens. In this paper, we proposed spatial modulated picosecond laser parallel processing method to prepare a superhydrophobic quasi-periodic MLA on fused silica. By using a spatial light modulator, the picosecond laser was shaped to multi-focal spots and line-shape beam, respectively, which improved the fabrication efficiency. The line-shape beam was the key to induce micro-nanostructures on the smooth MLA and keep the optical performance of the microlens. The results showed that the surface roughness of the microlens region was less than 100 nm. Combing with shaping picosecond laser processing and chemical treatment, the superhydrophobic MLAs showed the excellent anti-fogging and self-cleaning properties. The average contact angle of the superhydrophobic MLAs was 162.3°. The superhydrophobic MLA showed low adhesion to water droplet (<10 μN) and low contact angle hysteresis (2.1° ± 0.7°). We believe shaping picosecond laser parallel processing method is a flexible and low-cost approach to prepare superhydrophobic micro-optical elements on fused silica.