The experiment was carried out in the salt ponds (containing three types of soil: mild, moderate, and severe saline-alkali soil) at the experimental farm of the College of Agriculture, Yangzhou University. Using the salt-tolerant rice variety Nangengyan 1 as the experimental material, two irrigation and drainage treatments (T1 and T2) were set up to explore the impacts of different irrigation and drainage methods during the ponding period in coastal saline-alkali land on soil salinity and rice yield. T1: The soil in the salt ponds was plowed once; after 24 hours, a 3-4 cm water layer was irrigated; after another 24 hours, the field was allowed to dry; after 12 hours, a 3-4 cm water layer was irrigated again, and after 24 hours, the water was drained; this cycle was repeated twice. T2: The soil in the salt ponds was plowed twice; after 48 hours, a 3-4 cm water layer was irrigated; after another 48 hours, the field was harrowed to a depth of 5 cm and then allowed to dry; after 12 hours, a 3-4 cm water layer was irrigated again, and after 24 hours, the water was drained; this cycle was repeated three times. The results showed that the desalination rates of mild, moderate, and severe saline-alkali soils under T1 treatment were 20.3%, 25.7%, and 34.5% respectively; under T2 treatment, they were 24.5%, 32.4%, and 42.4% respectively. It can be seen that both irrigation and drainage treatments had good desalination effects, with T2 treatment showing a better effect. As the degree of salt stress increased, the population tiller number, tillering panicle rate, leaf area index, dry matter weight, effective panicle number, grains per panicle, seed setting rate, 1000-grain weight and yield of rice at the jointing, heading, and maturity stages showed a decreasing trend, while the harvest index showed an increasing trend. Compared with T1 treatment, T2 treatment increased the population tiller number, tillering panicle rate, leaf area index, dry matter weight and rice yields (with increases of 1.2%, 6.0%, and 9.1% respectively) at key growth stages under mild, moderate, and severe saline-alkali conditions. Compared with mild saline-alkali land, the reductions in rice yield under moderate and severe saline-alkali conditions were 17.4% and 31.1% respectively, mainly due to its positive effects on each component of rice yield. This study indicates that reasonable irrigation and drainage methods during the ponding period help to rapidly reduce soil salinity in coastal saline-alkali land and thereby increase rice yield.