Abstract Microlens array (MLA) has been widely used in optoelectronics field due to its characteristics of superior light extraction performance. However, most fabrication methods for MLA require heat or complicated processes and expensive equipment, which are not suitable for large-area, morphology-tunable MLA. This paper presents a new fabrication method for self-aligned MLA via multi-functional electrohydrodynamic (EHD) printing (direct-writing and drop-on-demand printing). The former creates a heterogeneously wettable surface for droplet self-aligning, and the latter precisely tune the droplet volume for MLA forming. This process is a versatile tool for MLA fabrication that inherits high resolution of EHD printing and morphology tunability from self-aligning process. By tuning the pattern of the confined zones and drop volume in each zone, MLA with different bottom shape, cell size, aspect ratio and filling factor have been generated, and their effects on light extraction have been discussed in detail. Finally, the self-aligned MLA with filling factor up to 99.3% reaches a light extraction enhancement of 49%, demonstrating their great potential in OLED light extraction.