The development of natural antioxidants to replace synthetic compounds is attractive. Perilla frutescens leaves were proven to be rich in antioxidants. The extraction of antioxidants from Perilla leaves via ultrasonic-assisted extraction (UAE) based on choline chloride-based deep eutectic solvents (DESs) was studied. Firstly, several DESs were prepared, and their extraction effects were compared. Secondly, the extraction process was optimized by single-factor experiments and response surface methodology (RSM). Finally, the optimization results were verified and compared with the results of traditional solvent-based UAE. The effects of solvents on the surface cell morphology of Perilla frutescens leaves were characterized by scanning electron microscopy (SEM). Choline chloride-acetic acid-based DES (ChCl-AcA) extract showed a relatively high ferric-reducing antioxidant activity (FRAP) and 2,2-diphenyl-1-picrylhyldrazyl radical scavenging rate (DPPH). Under the optimal operating conditions (temperature 41 °C, liquid-solid ratio 33:1, ultrasonic time 30 min, water content 25%, ultrasonic power 219 W), the experimental results are as follows: DPPH64.40% and FRAP0.40 mM Fe(II)SE/g DW. The experimental and predicted results were highly consistent with a low error (<3.38%). The values of the DPPH and FRAP were significantly higher than that for the water, ethanol, and butanol-based UAE. SEM analysis confirmed that ChCl-AcA enhanced the destruction of the cell wall, so that more antioxidants were released. This study provides an eco-friendly technology for the efficient extraction of antioxidants from Perilla frutescens leaves. The cytotoxicity and biodegradability of the extract will be further verified in a future work.