Objective This study aims to address the risk of missed detection due to trace contamination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the surfaces of cold chain food and packaging materials by developing a highly sensitive and quantifiable multiplex detection method. Method Based on multi-chip digital PCR (cdPCR) technology, we simultaneously targeted the ORF1ab, N, and E genes of SARS-CoV-2. Various parameters were optimized, including primer concentration, probe, and annealing temperature, and evaluated the methodological performance. Additionally, the analysis of viral nucleic acid load in cold chain food and packaging materials were simulated. Results The multi-cdPCR detection method can simultaneously identify all three gene fragments of the novel coronavirus. The detection limit for the ORF1ab gene is 1.36 copies/μL, while the detection limits for the N and E genes are both 0.96 copies/μL. This method exhibits high specificity and accuracy, with a coefficient of variation of less than 1.7%, demonstrating good repeatability. In blind sample testing of 70 suspected positive samples, the positive detection rates were 77.8% for multi-cdPCR and 27.8% for real-time fluorescence quantitative PCR. Our findings indicate that this method can be effectively applied to analyze viral contamination on the surfaces of cold chain food and packaging materials, with temperature variability influencing viral nucleic acid load. Conclusion This study successfully optimized and established a multi-cdPCR method suitable for detecting low viral loads of SARS-CoV-2 in food and packaging materials. This method provides valuable technical support for the safe supervision of viral contamination in cold chain food.