Perilla is herbaceous plant, functional food, and nutraceutical product with antioxidant properties. The objective of this study was to investigate the growth, reflectance indices, and antioxidant properties of P. frutescens species in response to fertilizer and salicylic acid (SA) applications. Two independent experiments were carried out in an environmentally controlled greenhouse: (1) pots of red-leaf and green-leaf cultivars divided into four groups treated with 10-30-20 (10N-13.1P-16.6K), 15-10-30 (15N-4.4P-24.9K), 20-20-20 (20N-8.7P-16.6K), and 30-10-10 (30N-4.4P-8.3K) fertilizers for periods of 10 weeks, and (2) pots of red and green Perilla cultivars divided into five groups treated with 0 (control), 125, 250, 500, and 1,000 µM of SA for periods of 7 weeks. Wide variations occurred in the agronomic performance, soil-plant analysis development (SPAD) value, adjusted normalized difference vegetation index (NDVI), maximal quantum yield of PSII photochemistry (Fv/Fm), and antioxidant activity of the two Perilla varieties. All the measured traits were higher in green than in red Perilla under identical fertilizing, and all agronomic traits in green and red Perilla plants subjected to 125 and 500 μM SA were better than in controls. The SPAD and NDVI values of all plants increased as N% increased, the lowest Fv/Fm values of all plants were observed under 15-10-30 fertilizer treatment, the lowest NDVI values were detected in controls, and the Fv/Fm values of all plants decreased under 1,000 μM SA treatment. These indices can be used as indicators to characterize the physiology of these plants and are suitable for evaluating their growth and development under specific fertilizer and SA treatments. Green Perilla leaf extract (PLE) contained higher rosmarinic acid (RA) concentration in each fertilizer treatment, and higher total phenolic (TP) and RA concentration in each SA treatment. However, red PLE contained higher caffeic acid (CA) concentration than green PLE in each fertilizer and SA treatment, implying that their two genotypes exhibited different abilities and specificities of photosynthetic metabolites, and that different varieties may prepare for 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity by up-regulating TP, RA, and CA concentration differently. Thus, Perilla plants can be used as health foods due to high TP, RA, and CA concentration. To produce Perilla efficiently in industrial applications, we undertook to determine the optimum N-P-K fertilizer ratio and SA application for maximizing the growth and accumulation of TP, RA, and CA in Perilla plants.