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 10$$min with an accuracy of greater than 95%.