Objective Using the advantages of zebrafish embryo transparency for live imaging, the role of imatinib in the development of blood vessels and nerves in zebrafish was studied. Methods First, we investigated the safe concentration range of imatinib for zebrafish in the blood vessel and neuron development stage using wild type zebrafish embryos. Within the safe concentration range, transgenic zebrafish embryos with a labeled vascular system were treated with imatinib. Moreover, endothelial cell and neuron co-labeled zebrafish were treated with imatinib to study the specificity for angiogenesis inhibition. The molecular mechanism of imatinib-inhibited angiogenesis was investigated. Results Imatinib concentration below 100 μg / mL was not lethal to zebrafish embryos. In this concentration, imatinib significantly inhibited the development of zebrafish intersegmental vessels (ISVs), including the process of ISV lumenization and the proliferation of endothelial cells. Additionally, imatinib had no significant effect on motor neurons and neuronal precursor cells. Moreover, gene expression analysis showed that imatinib was able to significantly inhibit vegfr2 and pdgfrα mRNA expression. Conclusions Imatinib significantly inhibited angiogenesis in zebrafish embryos by regulating VEGF and PDGFR signals.