Cryptosporidium and Giardia are two common species of pathogenic protozoan, seriously endangering the water quality. Former work indicated that compared to the USEPA method 1623, the procedure using membrane filtration-elution as a concentration method for detection of Cryptosporidium and Giardia attained better recovery and lower cost. Several improvements of membrane filtration-elution step as well as immunomagnetic separation (IMS) step were investigated and an optimal method for detection of Cryptosporidium and Giardia in wastewater reuse system was recommended in this study. The experimental results showed that overnight soak of membrane after scraping and vortex agitation before elution could enhance and stabilize the recovery. Increasing turbidity to 4NTU by adding kaolin clay could effectively improve the recovery of low-turbidity water. Washing concentrate after centrifugation and twice acid dissociation both reduced the impact of water quality. Protozoan in different water samples were detected by this optimal method, and recovery of Cryptosporidium and Giardia are above 70% and 80% respectively, far beyond the acceptance of method 1623.