The risk of fungal pollution in drinking water has been paid attention. Solar/chlorine dioxide (ClO2) combined system is an environment-friendly, economical and efficient disinfection method, especially for countries and regions that are economically backward and still exposed to unsafe drinking water. In this paper, the kinetics, influencing factors, mechanism and regrowth potential of inactivated Aspergillus niger (A. niger) spores by solar/ClO2 were reported for the first time. The inactivation curve can be divided into three stages: instant inactivation within 1–2 min, slow linear inactivation and finally a tail. The synergistic factors produced by solar/ClO2 in terms of log reduction and maximum inactivation rate were 1.194 and 1.112, respectively. The inhibitory effect on the regrowth of A. niger spores inactivated by solar/ClO2 was also stronger than that by ClO2 alone. Strongly oxidizing reactive species produced by solar/ClO2 accelerated the accumulation of endogenic reactive oxygen species (ROS) caused by oxidation stress of A. niger spores, improving the inactivation ability of the system. The inactivation order of A. niger spores was: loss of culturability, accumulation of intracellular ROS, loss of membrane integrity, leakage of intracellular species and change of morphology. The inactivation performance of solar/ClO2 was better than solar/chlor(am)ine according to the comparison of inactivation efficiency and regrowth potential. Results also suggested that solar/ClO2 process was more suitable for the treatment of ground water sources.