Plant autophagy plays an important role in response to abiotic stress. In this study, the relationship between autophagy related genes and reactive oxygen species (ROS) production was analyzed using physiological and genetic methods in model plant Arabidopsis. The results suggest that the leaves were photo-bleached, ROS production was induced and abundant cell death was accumulated in Arabidopsis wild-type Col-0 seedlings after 3 days salt stress. Quantitative real-time PCR analysis indicated that the expression of autophagy related genes were induced during salt stress. Autophagy participate in regulation defense mechanism in response to salt stress. Further studies suggest that the leaves were seriously photo-bleached, abundant cell death and ROS were accumulated in two Arabidopsis autophagy mutant seedlings (atg 2 and atg 5) after 3 days salt stress. Taken together, our results suggest that autophagy primarily regulate the ROS production in response to salt stress.