Lemon balm (Melissa officinalis L.), a member of Lamiaceae family, is an important medicinal plant that has many useful properties. Micronutrients are necessary in low dose for the growth and the development of plants. Present research was conducted to study the effects of micronutrients including manganese (Mn) and copper (Cu) on morpho-physiological traits and essential oil of lemon balm. Field trials were established in 2015 at Shahrekord (50°56^/ E 32°18^/ N) South Western Iran. Experiment was arranged in a randomized complete block design with a factorial layout and three replications. Micronutrients concentrations (Cu and Mn in 0, 150 and 300 ppm) were employed since of planting to beginning of flowering of plants. Of the two micro nutrients, copper was more effective in stimulating the accumulation of Caryophyllene β, Citronellal, Geranial, Geraniol, Geranyl Acetate, Linalool and Neral. At 150 ppm, micro nutrients enhanced the production of citronellal, Chavicol. Although combination of Cu²⁺and Mn²⁺ at 300 ppm in some of essential oils like neral, e-caryophyllene, caryophyllene oxide and 14-hydroxy-Z-caryophyllene were more produced than 150 ppm combinations but most of essential oils significantly increased in 150 ppm concentration of micronutrients. Trans-piperitone epoxide was upper extracted in 300 ppm concentration of Mn²⁺ but in many combination this essential oil was no extracted in little concentration. Geranial, Geraniol, (E-) Caryophyllene, Caryophyllene oxide and Neral were the main components in all treatments.