Abstract: In recent years, a new water-saving controlled irrigation technique aiming at more heavy rains in the South of China is proposed. It can reduce irrigation cost and make full use of rainfall, but may lead to alternative stress of drought-waterlogging-drought for rice. It is unclear about the root changes affected by the alternative stress. Therefore, in this study, a pot experiment was carried out to determine the effects of alternative stress of drought and waterlogging at tillering stage on rice root anatomical structure. The differences of root aerenchyma, column, the root epidermal cell development and root epidermal thickness in rice underwaterlogging stress treatments and the conventional irrigation were analyzed. The rice experienced three phases of drought stress (heavy drought A1 and light drought A2) and heavy waterlogging stress (15 cm water layer, B). The results indicated that A1 and A2 promoted development of root aerenchyma earlier than conventional irrigation (C) at stage I of drought stress; The thickness of the outer layer of roots in A1 and A2 treatments were higher than C treatment. A1 at stage I had a significant impact on root anatomical structure of flooding stress at stage II of drought converted to heavy waterlogging (A1B, heavy waterlogging for 5 d at stage II), of which the diameter, total area of tube and the column area increased by 43.3%, 52.8%, 76.5%, respectively, compared to conventional irrigation at stage II (CC); And the number of catheter, catheter area and in the column area of A2B treatment （heavy waterlogging for 5 d at stage II） was lower than that of CC treatment. However, the rice root formed a small amount of aerenchyma under the condition of flooding stress at stage Ⅱ (CB, heavy waterlogging for 5 d at stage II). Effects of heavy drought and light drought stress at stage III (A1BA1 and A2BA2) after flooding stress on rice root anatomical structure were similar to the effects of drought stress at stage I. A1BA1 formed more gas cavity, and there was still much residual cortex parenchyma cells in cortex; A2BA2 also formed more regular gas cavity. The number of catheter, catheter diameter, vessel area, and the column area of roots in A1BA1 treatment increased by 30.30%, 0.74%, 30.24%, and 52.84% compared with CCC treatment (conventional irrigation at stage III). The number of catheter and columns area of A2BA2 treatment increased compared with CCC treatment, and the catheter number and total area and column area of CBC treatment increased by 30.30%, 5.37% and 14.31%, respectively. Cortical cells of A2BA2 treatment were developed well with thick wall, and cortical cells of CBC treatment were also developed well but partial disordered. Therefore, short-term drought stress could improve the development of root aerenchyma, but could not decrease the waterlogging tolerance of rice. The anatomical changes might express post-effect of drought stress on rice root growth and a certain degree of drought and waterlogging stress played a positive role in improving the ability of late rice. The research could provide a valuble information for water-harvesting and controlled irrigation technology.