Growth-Stage-Specific Soil Fertility and Its Contribution to Rice Yield Under Agronomic Measures in Saline–Alkaline Paddy Fields

Reclaiming saline–alkaline soil is critical for food security and land expansion. While paddy rice is the key pioneer crop for remediation, the soil fertility–yield relationship remains poorly understood. To optimize remediation strategies, this study evaluated soil fertility under 16 agronomic treatments—integrating irrigation quality, fertilizer regimes, and soil amendments—across three rice growth stages (tillering, heading, and maturity) in the Yellow River Delta using the minimum data set (MDS), integrated soil fertility index (SFI), and random forest models. Saline water irrigation increased soil salinity by 24.6%, while straw returning and desulfurization gypsum reduced salinity by 18.3% and 22.7%, respectively. Straw, biochar, and desulfurization gypsum significantly influenced soil organic carbon (SOC), total nitrogen (TN), inorganic nitrogen (NH4+-N, NO3−-N), and available phosphorus (AP), with effects varying across growth stages. Growth-stage-specific MDS indicators were significantly correlated with SFI based on the total data set (R2 = 0.70, 0.65, and 0.81, p < 0.01), and stage-specific SFI was significantly positively related to rice yield. Notably, heading-stage SFI, although relatively low, explained the highest yield variance (R2 = 0.51, p < 0.01) and prediction accuracy (%IncMSE = 25.22), especially under conventional NPK combined with full straw incorporation and desulfurization gypsum. These findings highlight the critical role of heading-stage soil fertility in regulating rice production, providing a targeted nutrient management blueprint for saline–alkaline paddy fields in the Yellow River Delta. Overall, this study offers a reliable scientific template to enhance yield and promote sustainable agriculture in comparable saline–alkaline paddy fields globally.