Droplet evaporation at the fruit surface is a common issue related to the efficiency of pesticide spraying as well as freshness preservation. Many works have been carried out demonstrating the impacts of substrate characteristics on the droplet profile, wettability, and evaporation properties in the field of industrial applications. However, the influences of specific fruit skin on the droplet evaporation rate have been rarely studied. Thus, the present works aim to explore the effects of different surface micro-structures of fruits on the droplet properties experimentally through the 3D video microscope, drop shape analyzer, and infrared camera. Apple and peach have been selected respectively as two examples of waxy and hairy skins, and comparisons have been made focusing on the surface roughness, droplet profile including contact angle, contact area, and contact diameter, evaporation rate, and temperature distribution of droplets with a constant initial volume of 2ul. The results show that the differences in micro-structure for apple and peach surfaces have significant impacts on the droplet evaporation performance. A larger evaporation rate has been found for apple skin with three distinct phases including spreading, pinning, and shrinkage periods. However, the pinning phenomenon tends to be broken for the peach case due to the unique properties of super-hydrophobic surfaces and the existence of fluff. Moreover, lower values of temperature at the top center of a droplet can be always observed during the whole evaporating process with peak values of temperature gradient near the triple-phase region.