Abstract Zinc oxide (ZnO) nanomaterials are functional photocatalysts that show excellent photocatalytic activity, among which diverse morphologies, such as nanospheres, nanorods, nanoleaves, nanodisks, or nanoflowers, often possess different photocatalytic activities. In this study, we employed a simple ultrasonic treatment to controllably synthesize three types of three-dimensional (3D) fluffy ZnO nanoflowers with different nanostructures. Specifically, one nanoflower with smooth edges was formed via direct hydrothermal reaction without ultrasonic treatment (denoted as ZnO-0), and the other two with different jagged margins were obtained by ultrasonic treatment at 250 W and 950 W, respectively, before the hydrothermal procedure (denoted as ZnO-250 and ZnO-950). The results showed that the size, specific surface area, crystallite dimension, intrinsic donor defects and the signals of reactive radicals of ZnO nanoflowers all decreased with increasing ultrasonic intensity. Furthermore, the photocatalytic performance of such ZnO nanoflowers with similar morphologies but different nanostructures was investigated using methyl orange (MO) as a model pollutant. As expected, ZnO-0 possessed the highest photocatalytic activity with a kinetic constant of 0.0478 min−1, while the value decreased to 0.0251 min−1 and 0.013 min−1 for ZnO-250 and ZnO-950 under simulated sunlight irradiation, respectively, suggesting that the photocatalytic efficiency of ZnO nanoflowers decreased due to the ultrasonic treatment. These findings provide structural insight into the photocatalytic activity of ZnO nanoflowers.