Chloride channels represent a group of potential drug targets; their blockers showed significant protecting effect on impaired cells by modulating apoptosis, autophagy, and other cell signals. However, clinical drugs with chloride channel inhibitory properties have not yet been developed. Natural product extract becomes an underlying candidate satisfied the clinical requirements for its low toxicity, low cost, and abundant sources. Here, a fluorescence-based EYFP-H148Q/I153L-HeLa cell line model was constructed by molecular cloning and verified by real-time polymerase chain reaction and Western blotting assay. By using this chloride channel blocker screening model, seven hit compounds chosen from 6988 natural compounds showed the channel blocking activity. Then the hit compounds were further validated by electrophysiological patch-clamp analysis. Our study preliminarily identified PC-4 as a new chloride channel inhibitor and demonstrated the reliability and sensitivity of fluorescence-based high throughput screening technologies for discovery of biologically active compounds from natural herbal compounds.