Water scarcity and the overuse of chemical fertilizers present significant challenges to modern agriculture, critically affecting crop photosynthesis, yield, quality, and productivity sustainability. This research assesses the impact of organic fertilizer on the photosynthetic attributes, yield, and quality of pakchoi under varying irrigation water conditions, including fresh water and brackish water. Findings reveal that the modified rectangular hyperbolic model most accurately captures the photosynthetic reaction to organic fertilization, outperforming other evaluated models. The maximum net photosynthesis rate (Pnmax), yield, soluble sugar (SS), and soluble protein content (SP) all exhibited a downward-opening quadratic parabolic trend with increasing amounts of organic fertilizer application. Specifically, under fresh-water irrigation, the optimal Pnmax, yield, SS, and SP were obtained at organic fertilizer rates of 65.77, 74.63, 45.33, and 40.79 kg/ha, respectively, achieving peak values of 20.71 µmol/(m2·s), 50,832 kg/ha, 35.63 g/kg, and 6.25 g/kg. This investigation provides a foundational basis for further research into the intricate relationship between water salinity stress and nutrient management, with the goal of crafting more sophisticated and sustainable farming methodologies. The insights gained could significantly influence organic fertilizer practices, promoting not only higher yields but also superior quality in agricultural outputs.