Deep eutectic solvents (DESs) are considered as efficient and green solvents for the extraction of bioactive compounds from medicinal plants. In this work, a novel method of DES-based ultrasound-assisted extraction of bioactive compounds from Baphicacanthus cusia leaves (BCL) was established. Systematic screening and the morphology of the original and treated BCL were observed with scanning electron microscopy to determine the extraction efficiency of different solvents. The extraction conditions were optimized by Box–Behnken design (BBD) tests and the optimal extraction conditions were as follows: lactic acid/L-menthol ratio of 5: 2 (mol/mol), solid–liquid ratio of 80.0 mL/g and temperature of 60.5 °C. The extraction yields of tryptanthrin, indigo and indirubin reached 0.356, 1.744 and 0.562 mg/g, respectively. The results of a 2,2-diphenyl-1-picrylhydrazy (DPPH) radical scavenging activity test indicated the feasibility of DESs in the extraction of bioactive compounds. This study indicated that L-menthol/lactic acid was a green and efficient solvent for the extraction of bioactive compounds from BCL, and DES-based ultrasound-assisted extraction could be used as an effective application strategy for the extraction of bioactive compounds from medicinal plants.