This study was conducted at the research field of Islamic Azad University, Karaj Branch to investigate the effects of methanol on physiological indexes, yield and yield components and quality traits of soybean (Glycine max L.) in cropping seasons of 2012 and 2013. Aqueous solutions 0 (control), 7, 14, 21 and 28% (v/v) of methanol as well as three levels of irrigation 40, 65 and 70% soil water depletion were factors of this study. These solutions were applied over head three times in two-week intervals on foliage parts of soybean. According to the results, the maximum crop growth rate was observed in irrigation treatment after 40% water depletion. Also, this treatment produced the maximum leaf area index in all samplings and as the amount of light absorbed by the plant during growth stage is the determinant factor in dry weight production, the amount of cumulative dry weight production was higher compared to the other treatments. Also, with the increase in stress intensity, the amount of pod growth rate decreased, as the other growth indexes. Moreover, the biological yield had reduction in the second year compared to the first year. The cause can be probably related to the increase in average temperature and lack of rainfall during flowering and pod stages of soybean in this year. Finally, it has been recognized that for the qualitative traits, the treatments with the highest amount of seed oil content have the lowest amount of seed protein content.