Three novel modified advanced oxidation process systems including ascorbic acid-, pro-oxidants- and ascorbic acid-pro-oxidants-modified Fenton system were utilized to study the disinfection efficiency on Cryptosporidium-contaminated drinking water samples. Different concentrations of divalent and trivalent iron ions, hydrogen peroxide, ascorbic acid and pro-oxidants at different exposure times were investigated. These novel systems were also compared to the classic Fenton system and to the control system which comprised of only hydrogen peroxide. The complete in vitro mechanism of the mentioned modified Fenton systems are also provided. The results pointed out that by considering the optimal parameter limitations, the ascorbic acid-modified Fenton system decreased the Cryptosporidium oocytes viability to 3.91%, while the pro-oxidant-modified and ascorbic acid-pro-oxidant-modified Fenton system achieved an oocytes viability equal to 1.66% and 0%, respectively. The efficiency of the classic Fenton at optimal condition was observed to be 20.12% of oocytes viability. The control system achieved 86.14% of oocytes viability. The optimum values of the operational parameters during this study are found to be 80 mgL−1 for the divalent iron, 30 mgL−1 for ascorbic acid, 30 mmol for hydrogen peroxide, 25 mgL−1 for pro-oxidants and an exposure time equal to 5 min. The ascorbic acid-pro-oxidants-modified Fenton system achieved a promising complete water disinfection (0% viability) at the optimal conditions, leaving this method a feasible process for water disinfection or decontamination, even at industrial scales.