Copy number variation (CNV), including genomic deletions and duplication, has been associated with many kinds of diseases. It is crucial to precisely quantify the copy number variation of samples among patients, which may guide treatment. Digital PCR (dPCR) enables high-resolution CNV analysis through the ultraprecise absolute quantification of specific nucleic acid sequences. We explored a platform named digital CNV detection chip (DCD-chip), which can simultaneously and absolutely quantify the GPR146 and RPPH1 genes with amounts as low as 1.4 copies per μL. Finally, we verified that DCD-chip was more accurate than qPCR when the samples were diluted to a certain extent, which indicated the powerful quantification capacity of our DCD-chip platform.