Rice cultivation has the ability to improve saline soils. However, the effects of long-term rice cultivation on saline soil chemistry, salt ions, root characteristics, and aggregate formation remain unclear. In this study, the impact of different planting durations (1, 3, 5, 8, and 10 years) on the spatial and temporal transport of soil salts, soil chemical properties, distribution and stability of aggregates, root characteristics, and yields, were assessed. Long-term rice cultivation reduced soil pH, exchangeable sodium percentage (ESP), and EC in the 0-60cm soil layer compared to 1Y (5.45%, 61.57%, and 81.87% reduction in topsoil (0-20cm) and 8.54%, 72.82%, and 71.94 in subsoil (20-60cm), respectively). However, the soil organic matter (OM), alkaline nitrogen (AN), phosphorus (AP), and potassium (AK) increased (217.09%, 90.18%, 89.23%, and 179.18% increase in topsoil and 223.72%, 81.24%, 174.28%, and 172.57% increase in subsoil, respectively). Additionally, the Cl-, K+, and Na+ in the soil gradually leached downward with the increase in the duration of rice cultivation (55.87%、36.08%、59.80%). Simultaneously, the increased duration markedly elevated the soil macroaggregate content (11.43%-20.04% by dry-sieving and 53.48%-288.09% by wet-sieving), clayey grain content (59.17%-198.33%), and soil aggregate stability, especially for 8Y and 10Y. The improved soil structure and root characteristic under long-term rice cultivation conditions increased the yield (28.89-54.81%). Partial least squares path model displayed that rice cultivation affected the aggregate stability, root characteristics, and rice yield via the corresponding chemical properties (pH, EC, and ESP), nutrient contents (AN, AP, AK, and SOM), and salt ion contents (Cl-, K+, and Na+). These findings are critical to understanding aggregate formation in saline soils.