A simple and environment-friendly approach to prepare zinc oxide nanoaggregates was achieved by employing ethylene glycol–H2O as the reaction medium. The composition and structure of the as-fabricated ZnO products were confirmed using X-ray diffraction, scanning and transmission electron microscopy, X-ray photoelectron spectroscopy, and nitrogen adsorption measurements. By tailoring the volume ratio of ethylene glycol to water, coral-like, flower-like, and nanoparticulate ZnO nanoaggregates were successfully synthesized. The impact of the structure of the as-obtained ZnO nanoaggregates on the photocatalytic degradation of ciprofloxacin was further studied. Under simulated solar light irradiation, the photocatalytic removal rate of coral-like, flower-like, and nanoparticulate ZnO nanoaggregates for ciprofloxacin was 45%, 80%, and 90%, respectively. The reactive species trapping experiment result indicated that the generated holes, OH−, and ·O2− active species mainly contributed to the degradation of ciprofloxacin. On the basis of photoluminescence spectra and photo/electrochemical measurement results, the prevention of electron-hole recombination and the rapid charge transfer upon the ZnO nanoparticle aggregates resulted in their efficient photocatalytic activity. [Figure not available: see fulltext.].