In 2018, Longjing-31 of Japonica rice variety was planted in Qing'an County of Heilongjiang Province for the rice flooding experiment in cold region. At the jointing and booting stage, heading and flowering stage, three flooding depths (1/3 plant height, 2/3 plant height, and total plant height) and two flooding durations (3 d and 7 d) are designed for 12 flooding treatments, respectively. During the experiment, the tiller number before and after flooding, the plant height, LAI (leaf area index), dry matter, grain number per panicle, seed setting rate, 1 000-grain weight, and yield are measured and comparative analysis is conducted. The results are shown below. 1) After flooding, the average increase of plant height, LAI, and dry matter is higher than that of the CK (control check), which indicates that the moderate waterlogging stress could promote the growth of rice plant to some extent. Compared with the CK, the growth degree of all items in jointing and booting stage is lower than that in heading and flowering stage. 2) Different waterlogging stress leads to the reduction of Japonica rice yield. The yield is reduced most seriously after 7 d of total submergence at the jointing and booting stage, the number of grains per ear is only 55, and the 1 000-grain weight is 16.9 g, which are far lower than those of the CK, so the yield reduction rate is as high as 70%. The yield is reduced seriously after 7 d of total submergence at heading and flowering stage, the number of grains per ear is 71, the 1 000-grain weight is slightly lower, but the number of effective ears per unit area is 2.83 × 106, which is the least in all treatments, so the yield reduction rate is 57%. The average yield reduction rates of three flooding depths(1/3 plant height, 2/3 plant height, and total plant height) are 16%, 18%, and 48%, respectively, and the average yield reduction rates of durative waterlogging for 3 d and 7 d are 21% and 33%, respectively. On the whole, the reduction of rice yield increases with the deepening and lengthening of waterlogging. 3) Under the flooding stress, the decrease of rice yield at jointing and booting stage is greater than that at heading and flowering stage, and the main yield components leading to yield reduction in the two growth stages are the number of grains per ear and the number of effective ears per unit area, respectively.