Abstract: The rice seedlings of two different drought-resistant rice varieties, “Xiangfengzao119” (drought tolerant) and “Aihua No. 5 (drought sensitive), were treated with different concentrations of PEG-6000 (0 g·L^-1, 50 g·L^-1, 125 g·L^-1, 200 g·L^-1), and the morphological and physiological indexes such as root volume, maximum root length, lateral root length, adventitious root length, total root length, root quantity, root POD activity and relative permeability, were determined. The results show inhibiting effect of severe drought (200 g·L-1 PEG-6000) on roots morphological indexes except for root quantity of two rice varieties with more significant effects on drought sensitive variety. The rice roots morphological indexes increase with PEG-6000 treatment time, and make differences among different PEG-6000 concentrations after 3~4 d for treatment. Root POD activity and relative permeability increase with increasing PEG-6000 concentration and treatment time. Drought tolerant variety presents faster increment in POD activity and lower relative permeability than drought sensitive variety. Seedling root system of drought tolerant variety grows well with thicker, longer and stronger roots compared with that of sensitive variety. The results suggest root quantity and relative permeability should not be as indexes of drought tolerance selection.