Isopropyl 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate (IDHP) is the core active substance of salvia miltiorrhiza in disease treatment. The significance of our work lies in evaluating the ameliorating effects of IDHP on hypoxia-induced injury and investigating its mechanisms. We examined the morphology, dopamine neurons (DANs), cerebral vessels, and behavior of zebrafish larvae administrated by IDHP/VHC after hypoxia-induction. We next sought to explore its anti-hypoxic mechanisms via transcriptome analysis and qPCR experiments. The results indicated that hypoxia-induced injuries, including decreased length of DANs, number of cereal vessels, total swimming distance, and average swimming speed, were all alleviated by IDHP. Furthermore, transcriptome analysis provided a sign that IDHP most likely played the anti-hypoxic role through the neuroactive ligand-receptor interaction (NLRI) signaling pathway. Consistently, expression of related genes, such as f2rl1.1, p2ry10, npy1r, ptger2b, ptger2b, pth2rb, and nmur1a, was downregulated by hypoxia induction and recovered after IDHP administration. Therefore, we speculated that, via regulating NLRI, IDHP reduced inflammation, promoted angiogenesis, modulated blood pressure and flow, and inhibited cell apoptosis, and eventually played an anti-hypoxic role.