The effects of different application rates of humic acid compound fertilizer (HA) on the yield and physiological characteristics of pepper (Capsicum frutescens L.) were studied in this paper. The results showed that different application rates of (HA) could affect the physiological activities and yield of pepper. The nitrate reductase activity (NRA) and peroxidase (POD) activity were improved with increasing application rate, but the change rate of NRA was reduced gradually. POD activity in inorganic compound fertilizer treatment was improved significantly when the application rate of fertilizer was higher than 0.3 g.kg-1, but that in HA treatment changed smoothly. Superoxide dismutase (SOD) activity was improved significantly when the application rate of fertilizer was lower than 0.2 g.kg-1, and decreased gradually when the application rate was higher than 0.2 g.kg-1. The change of transpiration rate was consistent with that of SOD activity. The relationship between the application rate of fertilizer and the yield of pepper could be described with quadratic curve regression model. According to the equation, the highest application rate of HA should be 0.27 g.kg-1, and the highest yield of pepper could reach 165.22 g per pot.