The invention belongs to the technical field of gene detection, and specifically relates to a fluorescent PCR detection method for clostridium difficile toxin genes, as well as a primer and a kit of the fluorescent PCR detection method. The primer has good corresponding specificity, proper length and efficiency in transcription, and can not form a secondary structure, the primer contains complementation of not more than four continuous four basic groups; the testing coincidence rate obtained by adopting the primer is 98.6%, and the detection sensitivity can achieve 100copies/mL. According to the detection method, clostridium difficile DNA in a specimen, such as an excrement specimen, can be easily and conveniently extracted, and the genes of clostridium difficile toxins A and B are detected; the specific amplification primer and a fluorescence probe are adopted, so that the detection sensitivity and the specificity are greatly improved, the defect of insufficient specificity existing in an antibody and a cultivation detection method is overcome, and the problem of misdetection is also solved.