A pot experiment was conducted to investigate effects of addition rates of cotton stalk and the decomposed days of cotton stalk on the antioxidant enzyme activity and physiological parameters relative to photosynthesis of cotton. Results showed that substances from decomposed contton stalk inhibited the germination of seeds and the growth of seedling for cotton to some extent. With increasing decomposed days of cotton stalk,and rate of stalk added, the net photosynthetic rate (Pn), stomatal conductance (Gs), Transpiration rate(Tr) and intracellular CO2(Ci) in succeeding cotton leaves decreased respectively. When stalk addition rate was 10 g?kg-1, Pn value was slightly higher than control (without cotton stalk addition), while when stalk addition rates increased progressively, Pn value decreased correspondingly. At the addition rate of 90 g?kg-1, Pn value of succeeding cotton leaves decreased 26.8% and 43.4% respectively at 30\|day and 60\|day decomposed time. With increasing stalk rate and decomposed time, POD activity increase, SOD and root vigor was declined too, but MDA content in leaf was enhanced. The results suggested that the decomposing substances after cotton stalks returned to soil have autotoxic effect. Cotton seed germination and photosynthesis physiological activities were affected by decomposed substances of cotton stalks.