The zebrafish embryos were widely employed in genetics, development and drug discovery studies as miniatured animal models. Sorting of two-color fluorescent embryos is often required in large-scale experiments but it is challenging to manually sort with high efficiency. Here, we reported a high-throughput sorting system for two-color fluorescent zebrafish embryos. The embryos can be automatically loaded from a sample pool and sorted based on the average fluorescent intensity. The two-color fluorescent signals were split into two lines and detected by an area array camera. The system achieves the sorting of 100 embryos in less than 10min with an accuracy of greater than 95%.