The effect of acidolysis time, hydrochloric acid concentration, ozonization time and pH on the yield of indigo were investigated by single factor experiment using dried leaves of Baphicacanthus cusia (Nees) Bremek (DLB) as raw material. On this basis, the technological condition for preparing new indigo extract (NIE) by directional chemical conversion method was optimized by orthogonal experiment. Then, the physiochemical properties of NIE were analyzed by combustion assay, nitric acid assay, thin layer chromatography identification assay, moisture detection and water-soluble pigment observation assay. Moreover, UPLC-Q-TOF-MS/MS technology was utilized to compare chemical composition difference between the NIE and traditional indigo naturalis (TIN). Finally, NIE emulsion was prepared by ultrasound assisted high pressure homogenization method and its stability, antibacterial activity as well as antibacterial mechanism were evaluated. The experimental results showed that optimum process for preparing NIE were hydrochloric acid concentration of 2 %, ozonization time of 3 min, pH of 7 and acidolysis time of 1 h; Under this condition, the content and yield of indigo in the NIE were significantly improved, which could reach up to 42.6 ± 0.28 % and 2.26 ± 0.04 %, separately. NIE possessed similar physiochemical properties with TIN described in Chinese pharmacopoeia 2020, and had more diverse active ingredients than TIN. The prepared NIE emulsion demonstrated excellent stability, whether at dark or bright place, and no matter at low temperature (4 ℃) or room temperature (25 ℃), the particle size, PDI, pH and indigo content of which displayed little variation. In addition, the NIE emulsion owned good inhibitory activity against S. aureus, and its MIC and MBC values were 40 and 80 μg/mL, respectively. Moreover, NIE emulsion exhibited antibacterial effect by influencing cell membrane integrity, Ca2+-Mg2+-ATPase activity on the cell membrane and intracellular Ca2+ levels of S. aureus. All of above results will lay the foundation for the green and sustainable utilization of Baphicacanthus cusia (Nees) Bremek.