Digital PCR is an absolute quantitative technique that does not depend on reference material and standard curves, and is widely used in quantitative detection. In this study, three digital PCR platforms, including QX200 droplet digital PCR, Naica droplet chip digital PCR and DropDx-2044 microfluidic digital PCR, were used to determine the specific DNA sequence copy number of animal and plant samples. The throughput and cost of different digital PCR platforms were compared, and the characteristics of the three digital PCR platforms in DNA accurate quantitative detection were evaluated. The results showed that there were no significant differences in the applicability, linear correlation, accuracy and precision of the three digital PCR platforms for the quantitative detection of animals and plants. The Naica digital PCR platform has obvious advantages in terms of detection throughput, detection cost and ease of operation. This study provides a technical reference for laboratories to select an appropriate digital PCR platform for different types of sample detection.