In the middle and lower reaches of the Yangtze River, there is more rainfall in summer, especially in jointing stage of hybrid mid-season rice, so that rice is liable to suffer from waterlogging damage. In order to quantitively reveal the influence of flooding on hybrid mid-season rice growth, scientifically assess the yield loss caused by it, and to provide data base of the morphological, physiological characteristics and yield structure, those indexes presented higher correlation degree with relative yield could be used as key morphological and physiological indexes to indicate the yield reduction level at the jointing stage of hybrid mid-season rice after flooding, a cross test of flooding depth(a quarter, a half, three-quarters and full submerged) and waterlogging duration(3, 6 and 9 days) was done in the jointing stages of hybrid mid-season rice. The results showed that after submergence treatment, the rice height and the internode length all present elongation(the 1rd and 2th internode elongate mainly in the booting stage, the 2rd internode elongating faster), the yellow leaves number and the longest leaf length of plant increased significantly, which is significant linear positive correlation with the increase of flooding depth and waterlogging duration, A significant correlation of two variables with the first power exists among YPH (plant height growth), YIL(internode length), YYL(yellow leaves number), YLL(longest leaf length)and D(submergence days), H(submergence depth); as far as physiological characteristics, under the identical flooding duration, chlorophyll(Chla and Chlb) and soluble protein content of sword leaf was decreased with the increase of waterlogging duration, which has significant negative correlation with flooding depth, but the content of soluble saccharide was increased first and then decreased with the increase of flooding depth, while the MDA content in the sword leaf was significantly positively related with the increase of flooding depth, and in the root was increased first and then decreased when the flooding duration was 9 days, which the turning point was a half submergence depth. At the same time, the activity of SOD in the sword leaf and root was increased first and then decreased with the increase of flooding depth, the activity of POD in sword leaf presents the rising trend with the increase of flooding depth, moreover the severe the waterlogged depth was, the higher the amplification of POD activity could be, and that in root was increased first and then decreased with the increase of flooding depth, which the turning point was a half of submergence for 6 days, under the identical flooding duration. In light of the yield component, the seed setting rate reduced by more than 20% and yield decreased by 19% than that of the control when the rice run into quarter of submergence for 6 days at the jointing stage. Through gray correlation and cluster analysis in this research, it was concluded that Chlb, soluble protein and Chla content could be used as key physiological indexes in evaluating waterlogged and reduction of yield degree after flooding.