The fluorescence staining method and scanning electron microscopy (SEM) were used to study the effect of ozone (O3) inactivating Cryptosporidium in water and cell ultrastructures variation to shed light on the mechanism of inactivation preliminarily. Results indicated that O3 had a stronger inactivating capability. When the concentration of O3 was above 3.0 mg/L and the contact time was up to 7 min, a significant inactivating effect could be achieved. The turbidity on inactivation effects was also found to be statistically significant in artificial water. With increases in turbidity, the inactivating effect decreased. Inactivation rate improved with a temperature increase from 5 to 25 degrees C, but decreased beyond this. The inactivating capability of O3 was found to be stronger under acidic than that under alkalic conditions. When the concentration of organic matter in the reaction system was increased, the competition between Cryptosporidium and organics with O3 probably took place, thereby reducing the inactivation rate. In addition, the cellular morphology of Cryptosporidium varied with different contact times. At zero contact time, cells were rotundity and sphericity, at 60 sec they became folded, underwent emboly, and burst at 480 sec, the cell membrane of Cryptosporidium shrinked and collapsed completely.