Cryptosporidium and Giardia in reclaimed water are endangering the health of human beings by direct and indirect ways. Compared with traditional disinfection measures, flocculation, clarification and filtration can remove the pathogenic protozoan from wastewater more effectively. The factors affecting the removal of pathogenic protozoan from secondary effluent in flocculation process, including type and dosage of flocculant, pH, temperature and other reaction conditions were studied. The experimental results showed that the effectiveness of pathogenic protozoan removal appeared to be good at pH 6 - 8 and bad at low temperature. The effectiveness increased with the increase of ferric chloride dosage. Aluminium sulphate and poly aluminium chloride gave better performance in removal of pathogenic protozoan at the dosage of 70 mg/L and 20 mg/L respectively.