Pathological retinal angiogenesis is a major cause of vision impairment and blindness. The development of pathological angiogenesis in ischemic retinopathy is linked to oxidative stress and dysregulated inflammatory response, in which microglia play a vital role. Cryptotanshinone (CTS), a bioactive compound found in Salvia miltiorrhiza, demonstrates protective characteristics such as antioxidant and anti-inflammatory properties. Therefore, it might influence abnormal retinal angiogenesis, the pathophysiological mechanisms of which are yet not well known. Overactivation of the stimulator of interferon genes (STING), a DNA-sensing adaptor protein, in microglia is a critical mechanism in ischemic retinopathy. Here, we showed that CTS treatment substantially reduced microglial activation and pathological retinal angiogenesis in a mouse model of oxygen-induced retinopathy (OIR). The integration of network pharmacology, bulk RNA sequencing, single-cell RNA sequencing analyses, and verifying experiments revealed a strong association between the suppression of the STING pathway in microglia and the protective effect of CTS on ischemic retinopathy. Mechanistically, firstly, CTS suppressed the release of cytosolic mitochondrial DNA (mtDNA), a causative factor for STING activation, by suppressing mitochondrial ROS-induced mitochondrial damage. Secondly, CTS inhibited STING’s translocation from the ER to the Golgi and subsequent activation of the downstream TBK1-NF-κB pathway by binding to its Ser162 site. Finally, CTS accelerated lysosome-mediated STING protein degradation by improving lysosomal function. Intriguingly, the inhibitory effects of CTS on microglial activation and retinal neovascularization were eliminated by STING activation. Furthermore, CTS treatment did not provide further protection in Sting deficient (Sting−/−) OIR mice. Collectively, our study indicated that CTS, a natural inhibitor of STING, alleviated ischemic retinopathy by inhibiting the mtDNA-STING-NF-κB signaling pathway via multifaceted mechanisms in microglia.