Abstract: To maintain soil quality under long-term saline water irrigation, the influence of manure on soil physical properties was examined. Long-term saline irrigation has been conducted from 2015 to 2024 at the Nanpi Experimental Station in the Low Plain of the North China Plain, comprising four irrigation treatments: irrigation once at the jointing stage for winter wheat with irrigation water containing salt at 1 g·L^–1 (fresh water), 3, 4 and 5 g·L^–1, and maize irrigation at sowing using fresh water. Manure application was conducted under all irrigation treatments, with treatments without manure application used as controls. The results showed that under long-term irrigation with saline water, the application of manure increased the soil organic matter content, exchangeable potassium, available phosphorus, and total nitrogen content in the 0–20 cm soil layer by 46.8%, 117.0%, 75.7%, and 45.5%, respectively, compared to treatments without manure application. The application of manure reduced soil bulk density. It also increased the proportion of water-stable aggregates and the abundance of bacteria, fungi, and actinomycetes in the tillage soil layer compared to the controls. Because of the salt contained in the manure, the application of manure had dual effects on soil salt content. During the winter wheat season, manure application increased soil salt content. The salt content was significantly reduced during the summer maize season, owing to the strong salt-leaching effects under manure application, resulting in a smaller difference in salt content between the manure and non-manure treatments. During the summer rainfall season, improvements in soil structure under manure application increased the soil desalination rate by 38.3%, 14.7%, and 21.3% compared to the no-manure treatments in the 0–40 cm, 40–100 cm, and 100–200 cm soil layers, respectively. The yield of winter wheat under manure application was slightly lower than that of the control, owing to the higher salt content during the winter wheat season. In contrast, the yield of summer maize improved by 3.9% under manure application, owing to the increased soil nutrient content and effective salt leaching. The annual yields of winter wheat and summer maize were similar for saline and freshwater irrigation treatments. The results of this study indicated that manure application helped maintain the soil physical structure, which is important for the long-term use of saline water. In practice, using manure with a low salt content is suggested to reduce the adverse effects of saline water irrigation on soil properties and achieve sustainable saline water use.