Botanical oils are staple consumer goods globally, but as a by-product of oil crops, meal is of low utilization value and prone to causing environmental problems. The development of proteins in meal into bioactive peptides, such as Perilla peptide, through biotechnology can not only solve environmental problems, but also create more valuable nutritional additives. In the present work, the hydrolysis process of Perilla meal protein suitable for industrial application was optimized with the response surface methodology (RSM) on the basis of single-factor experiments. Alcalase was firstly selected as the best-performing among four proteases. Then, based on Alcalase, the optimal hydrolysis conditions were as follows: enzyme concentration of 7%, hydrolysis temperature of 61.4 °C, liquid-solid ratio of 22.33:1 (mL/g) and hydrolysis time of 4 h. Under these conditions, the degree of hydrolysis (DH) of Perilla meal protein was 26.23 ± 0.83% and the DPPH scavenging capacity of hydrolysate was 94.15 ± 1.12%. The soluble peptide or protein concentration of Perilla meal protein hydrolysate rose up to 5.24 ± 0.05 mg/mL, the ideal yield of which was estimated to be 17.9%. SDS-PAGE indicated that a large proportion of new bands in hydrolysate with small molecular weights appeared, which was different from the original Perilla meal protein. The present data contributed to further, more specific research on the separation, purification and identification of antioxidant peptide from the hydrolysate of Perilla meal protein. The results showed that the hydrolysis of Perilla meal protein could yield peptides with high antioxidant activity and potential applications as natural antioxidants in the food industry.