Paddy cultivation has become a widely adopted approach for saline-sodic wasteland reclamation, aiming to mitigate the food crisis and enhance soil quality. Nevertheless, the impact of long-term paddy cultivation on the interplay between soil quality, microbial metabolic functions, and soil ecosystem multifunctionality (EMF) remains unclear. Here, we evaluated soil physicochemical properties, the abundance of 132 biomarker functional genes, and soil EMF across a 78-year period of saline-sodic paddy cultivation. After 78 years of paddy cultivation, soil pH and electrical conductivity (EC) decreased by 43.38% and 93.02% compared to saline-sodic wasteland (WL), respectively. Moreover, principal component analysis was used to select a minimal dataset of soil indicators and to establish a soil quality index (SQI). Significant positive correlations were observed between SQI and rice yield, implying that soil quality was the main factor driving increases in saline-sodic farmland. The Mantel test indicates that soil microbial biomass, SQI, and the availability of nutrients exhibit a significant positive relationship with the abundance and expression of genes related to carbon (C), nitrogen (N), and phosphorus (P) cycling, encompassing crucial biogeochemical processes like hemicellulose degradation, C fixation, N degradation, and organic P mineralization. This indicates that changes in soil physicochemical properties significantly affect biogeochemical cycling in saline-sodic soils. Differences in the abundance of microbial P core functional genes explained 41.9% of variation in soil EMF, followed by key soil physicochemical indicators (EC, available potassium, microbial biomass nitrogen, etc.) selected through random forest analysis. Further, we identified a key threshold for changes in soil EMF during long-term saline-sodic paddy cultivation, with EMF increasing for the first 20 years of restoration before decreasing thereafter. Finally, partial least squares path modeling revealed the roles of microbial functional genes and SQI in driving soil EMF before and after the threshold. Soil EMF is primarily influenced by the significant negative effects of P functional genes prior to the threshold value, whereas beyond the threshold, it is mainly affected by the positive effects of C functional genes. These findings provide insights into the functional restoration and sustainable development of saline-sodic agricultural ecosystems.