The invention relates to the field of PRC detection, in particular to a method for detecting three kinds of protozoa in duck manure by using multiple PCR, wherein the protozoa include Cryptosporidium baileyi, Cyclospora and Wenyonella philiplevinei. The detection method of the invention comprises: designing three pairs of specific premiers according to the ITS-1 gene of the Cryptosporidium baileyi, the 18S rRNA gene of the Wenyonella philiplevinei and the ITS-1+ fragment of the Cyclospora of ducks respectively; and quickly and accurately detecting the oocysts of the Cyclospora, the Cryptosporidium baileyi and the Wenyonella philiplevinei in the duck manure by multiple PCR reactions to identify and diagnose the Cryptosporidiosis, Cyclospora disease and coccidiosis of ducks. The detection method of the invention can detect the three kinds of protozoa at the same time, has high sensitivity and specificity, is more quick and economic than conventional PCR and can be used for the identification and diagnosis of duck intestinal protozoa disease, molecular epidemiological survey and waterborne Cryptosporidiosis and Cyclospora disease outbreak risk evaluation.