Provided are a ZnO-based substrate having a high-quality surface suitable for crystal growth, a method for processing the ZnO-based substrate, and a ZnO-based semiconductor device. The ZnO-based substrate is formed such that any one of a carboxyl group and a carbonate group is substantially absent in a principal surface on a crystal growth side. Also, in order for a carboxyl group or a carbonate group to be substantially absent, any one of oxygen radicals, oxygen plasma and ozone is brought into contact with the surface of the ZnO-based substrate before the crystal growth is started. Consequently, cleanness of the surface of the ZnO substrate is enhanced, thereby enabling fabrication of a high-quality ZnO-based thin film on the substrate.