In this paper, ZnO nanofilms are prepared on quartz substrate by ultrasonic spray pyrolysis (USP) technology. The effects of substrate temperature and deposition time on the micro-structural, morphological and optical properties of ZnO thin films are investigated in detail. Measurements indicate that the growth process of the film is as follows: Micro grains accumulation → grains’ expansion → grow into certain nanostructures under different temperature. Nanostructures of the film are as follows: Irregular broken hexagonal-like structure (<450∘C); coexisting of broken hexagonal- and sheet-like structure (450–500∘C); regular closed packed sheets-like structure (>500∘C). In addition, all results show that RMS roughness of the films is less than 20 nm. Moreover, the visible transmittance of these samples is higher than 90%. Which display that ZnO films with low roughness and excellent optical properties can be also fabricated by low-cost USP method.