Transparent microfluidic devices based on ZnO thin film/glass surface acoustic waves (SAWs) were explored for active surface cleaning based on its acoustofluidic performance. Acoustic waves generated from ZnO films on glass substrate were investigated and their acoustofluidic performance including transportation, jetting and nebulization were evaluated. Ash particles and starch solutions were used as model contaminants on the surface of the ZnO/glass SAW devices, and the mass loading of the contaminants on the device's surface was monitored using the SAW device with a high sensitivity of 280.0 ± 9.0 Hz/(μg/mm2). Active surface cleaning of the contaminants was demonstrated based on the transportation of water droplets, and optimized SAW powers were identified which caused strong interactions between water droplet and contaminants, thus effectively cleaning the surfaces. Studies of surface heating effects induced by SAWs showed that the cleaning efficiency was also influenced by the substrate temperature induced by SAW agitations.