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Droplet evaporation on rough substrates is ubiquitous in nature and has numerous technological applications, such as coating. To study the evaporation characteristics of nanodroplets on substrates with different rough structures, molecular dynamics simulations have been performed. Based on the Wenzel wetting model, three systems with different rough structures were constructed, in which the ratios of contact area (RCA) between substrates and nanodroplets were 33.3%, 50%, and 66.6%, respectively. The results indicate that the evaporation pattern of the nanodroplet in the system with RCA = 33.3% is the mixed mode, the evaporation pattern of the nanodroplet in the system with RCA = 50% is the constant-contact-radius mode, and the evaporation pattern of the nanodroplet in the system with RCA = 66.6% is the constant-contact-angle mode. Meanwhile, when the temperature of substrates (T) is suddenly raised from 0.67 to 0.83 ε/kB, followed by a corresponding rise in the temperature of nanodroplets, we find that temperature and evaporation rates of the nanodroplets increase with the increase in RCA in this period. Changes in RCA that lead to the changes in substrate wettability affect the heat transfer between nanodroplets and substrates. In particular, the more the substrate wettability, the higher the heat transfer efficiency. Moreover, the wettability of the substrate in the systems with RCA = 50% and 66.6% promotes the heat and mass transfer in the three-phase contact line region of the nanodroplets during the evaporation process, while the non-wettability of the substrate in the system with RCA = 33.3% suppresses the local heat and mass transfer. This work offers further knowledge of droplet evaporation on rough substrates, which, in turn, provides a reference for the process optimization of its technological applications. [ABSTRACT FROM AUTHOR]