Applying fertilizers correctly is crucial for enhancing soil fertility and crop productivity. Nonetheless, the long-term effects of slag-based gypsum (SBG) and commercial gypsum (CG) on soil fertility and crop yield remain poorly understood. Field experiments were conducted over six seasons with rice crops to investigate the impact of long-term application of four levels (300, 450, 600, and 750 kg ha-1) of SBG and CG, in conjunction with the recommended dose of fertilizer (RDF), on soil fertility, nutrient uptake, and rice yield. Long-term fertilization with varying levels of SBG and CG significantly influenced the overall rice yield, with the highest grain and straw yields recorded at 750 kg SBG ha-1 (6.90 +/- 0.14 and 9.59 +/- 0.33 t ha-1, respectively). The application of SBG and CG over the long term had minimal impact on soil pH while notably increasing nutrient uptake and soil fertility. There was a significant correlation between SBG, CG, and soil nutrients, except for soil pH and potassium (K). Principal component analysis (PCA) highlighted that the application of 450, 600, and 750 kg SBG ha-1, as well as 600 and 750 kg CG ha-1, exhibited distinct behavior and outperformed other doses concerning soil nutrients and their uptake. The long-term application of SBG and CG, in combination with RDF, led to an increase in soil fertility and rice yield. However, the long-term application of 450 kg SBG ha-1 yielded comparable results to 600 and 750 kg ha-1 of both SBG and CG, suggesting its efficacy over time.