Manganese oxide (MnOx) shows great potential in the areas of nano-electronics, magnetic devices and so on. Since the characteristics of precise thickness control at the atomic level and self-align lateral patterning, area-selective deposition (ASD) of the MnOx films can be used in some key steps of nanomanufacturing. In this work, MnOx films are deposited on Pt, Cu and SiO2 substrates using Mn(EtCp)2 and H2O over a temperature range of 80–215 °C. Inherently area-selective atomic layer deposition (ALD) of MnOx is successfully achieved on metal/SiO2 patterns. The selectivity improves with increasing deposition temperature within the ALD window. Moreover, it is demonstrated that with the decrease of electronegativity differences between M (M = Si, Cu and Pt) and O, the chemisorption energy barrier decreases, which affects the initial nucleation rate. The inherent ASD aroused by the electronegativity differences shows a possible method for further development and prediction of ASD processes.