The scarcity of freshwater, the increasing use of brackish water (B) for irrigation, and the judicious application of organic fertilizers have significant research and practical value for environmental science, water resource management, and clean production. This study investigated the combined impact of B, magnetized-ionized brackish water (MIB), and organic fertilizer on pakchoi (Brassica chinensis L.) growth, yield, and soil quality. Over a two-year period (2022–2023), this study explored the impacts of two types of irrigation water (B and magnetized-ionized brackish water, MIB) in combination with varying rates of water-soluble bio-organic fertilizer (0, 20, 40, 60, and 80 kg/ha, corresponding to treatments 0 through 4, respectively). The findings indicated that the application of 60 kg/ha of organic fertilizer greatly improved the growth rate of pakchoi in terms of plant height, leaf area index, and fresh weight. Moreover, under MIB irrigation, the fresh weight growth rate of pakchoi was superior to that observed under B irrigation. Notably, B irrigation necessitated additional fertilizer to maintain elevated levels of alkali-hydrolyzed nitrogen (AN) and soil quality. Furthermore, the use of organic fertilizer substantially enhanced soil quality, with AN, available phosphorus (AP), organic matter (OM), and soil quality index (SQI) demonstrating a strong positive correlation (P < 0.05). Mantel test analysis showed significant correlations (P < 0.05) between soil OM, SWC, AP, and pakchoi growth and yield. According to the partial least squares path modeling analysis, the use of organic fertilizer had a relatively minor effect on the yield and quality of pakchoi under B irrigation, with path coefficients of 0.088 and 0.298, respectively. However, under MIB irrigation, organic fertilizer enhances yield and quality by improving soil quality (path coefficients of 0.914). In conclusion, the application of MIB irrigation coupled with organic fertilizer contributed to sustainable soil fertility, enhanced crop productivity, and mitigated the environmental impacts associated with conventional irrigation and fertilization methods. Our research underscores the importance of supporting agricultural research and development focused on sustainable irrigation and fertilization methods for farmers and policymakers. This integrated approach offers a harmonious solution for optimizing crop yields and enhancing water use efficiency, and the reduction of in chemical pollutants within agricultural production systems.