Viral hepatitis is a common infectious disease caused by five viruses (hepatitis virus A, B, C, D, and E). Given the diversity of hepatitis virus, rapid screening and accurate typing of viral hepatitis are the prerequisites for hepatitis therapy. Here, a multicolor fluorescence system was constructed by combining with the multi-color fluorescence properties of CdSe/ZnS quantum dots (QDs, emission wavelengths: 525 nm, 585 nm and 632 nm) and the broad-spectrum fluorescence quenching performance of GO. Taking advantage of the specific recognition of ssDNA modified CdSe/ZnS QDs to target hepatitis virus DNA, the constructed system could effectively distinguish hepatitis A virus DNA (HAV-DNA), hepatitis B virus DNA (HBV-DNA), and hepatitis C virus DNA (HCV-DNA) in a homogeneous solution. Based on the different adsorption property of GO for ssDNA and dsDNA, the fluorescence Forster resonance energy transfer (FRET) process between ssDNA modified QDs and GO could be regulated. The fluorescence signal of the constructed system presented a sensitive response to HAV-DNA, HBV-DNA, and HCV-DNA content in the range of 1.0–192 nM, 8.0–192 nM, and 1.0–128 nM, respectively. The limit of detection for HAV-DNA, HBV-DNA, and HCV-DNA is 0.46 nM, 1.53 nM, and 0.58 nM. The constructed system can be used to screen hepatitis virus DNA in real samples, which provides an alternative strategy for rapid screening and diagnosis of viral hepatitis.