Fluorine stability in the soil is crucial to protecting the groundwater and the food chain from pollution by fluorine, which was abundantly present (762.78–1330.66 mg/kg) in soda saline-alkali soil areas of western Jilin Province. This study investigated the fluorine distribution and pollution level in soil. Two representative areas in Zhenlai County, namely Chagan and Hatu villages, were selected to gather soda saline-alkali soil profiles (0–20, 20–40, and 40–60 cm) from different cultivation years (i.e. 3, 5, 8, 10, 13, 15, 18, and 20). The results revealed that fluorine content in soil decreased with increasing cultivation years. In the soil profiles, fluorine and water-soluble fluorine concentrations followed the order of 40–60 > 20–40 > 0–20 cm, while the contents of exchangeable and organic matter-bound fluorine decreased with the increasing profile depth. Rice planting increased the content of macroaggregates with diameters >2 and 2–0.25 mm, which significantly improved the aggregate structure of the soil. The fluorine content was the greatest in microaggregate with particle sizes <0.053 mm in the aggregates' sizes. Rice planting in saline-alkali soil reduced the contents of water-soluble and exchangeable fluorine, while enhancing the content of organic matter-bound fluorine, thereby reducing the bioavailability of fluorine in the soil and the risk of fluorine migration through the groundwater. The degree of soil pollution decreased with increasing plantation years, and the soil became slightly polluted after 15 years of rice planting. The rice plants grew normally after years of improving fluorine-containing saline-alkali land, and the fluorine content was within the safe limit.