Hydrophobicity is abundant in nature and obtainable in industrial applications by roughening hydrophobic surfaces and engineering micropatterns. Classical wetting theory explains how surface roughness can enhance water repellency, assuming a droplet to have a flat bottom on top of micropatterned surfaces. However, in reality, a droplet can partially penetrate into micropatterns to form a round-bottom shape. Here, we systematically investigate the evolution of evaporating droplets on micropatterned surfaces with X-ray microscopy combined with three-dimensional finite element analyses and propose a theory that explains the wetting transition with gradually increasing penetration depth. We show that the penetrated state with a round bottom is inevitable for a droplet smaller than the micropattern-dependent critical size. Our finding reveals a more complete picture of hydrophobicity involving the partially penetrated state and its role in the wetting state transition and can be applied to understand the stability of water repellency of rough hydrophobic surfaces.