The detection of nuclear acid polymorphism has an important role in basic research and clinical application. The popular methods are PCR based on probe. Probe with cross-reactivity limits the application of traditional real-time quantitative PCR to quantitate allelic transcripts．Digital (d)PCR may overcome cross-reactivity defects, but available dPCR machines lack discrete optical channels, which limits the detection of more than two molecules. Colon cancer associated transcript 2 (CCAT2) is a non-coding transcript, encompassing rs6983267 SNP site. Here, we report a method based on two channels droplet digital PCR to quantitate three CCAT2 polymorphisms in one reaction. We designed a pair of primers and three hydrolysis probes including a reference and two competing probes. We successfully discriminated between the three CCAT2 transcript clusters. We took advantage of the cross-reactivity to provide a white space for more visible distinct clusters, although innate rain was detected. Labelling the reference probe with cross-reactivity probe resulted in more distinct clusters than the probe without cross-reactivity.