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In this paper, we numerically investigate drop impact on a micro-well substrate to understand the phenomena of non-wettability. The simulation is carried out by solving three-dimensional incompressible Navier–Stokes equations using a density projection method and an adaptive grid refinement algorithm. A very sharp interface reconstruction algorithm, known as the moment-of-fluid method, is utilized to identify the multi-materials and multi-phases present in the computation domain. Our simulations predicted that a micro-well with a deep cavity can significantly reduce a solid–liquid contact in the event of drop impact. The results from the drop impact on the micro-well substrate are compared with results from drop impact on a flat substrate. Significant differences are observed between these two cases in terms of wetted area, spreading ratio, and kinetic energy. Our simulation shows that under the same conditions, a drop is more apt to jump from a micro-well substrate than from a flat surface, resulting in smaller wetted area and shorter contact time. Based on the simulation results, we draw a drop jumping region map. The micro-well substrate has a larger region than the flat surface substrate. Finally, we present a comparative analysis between a flat substrate and a substrate constructed with a dense array of micro-wells and, therefore, show that the array of micro-wells outperforms the smooth substrate with regard to non-wettability and drop wicking capability.