The long-term utilization of inorganic fertilizers in pakchoi cultivation can result in increased nitrate levels, potentially posing health risks to human consumers. For this study, we investigated the efficacy of organic fertilizers as a promising alternative for enhancing soil structure, improving fertility, and increasing the yield of pakchoi. A two-year field trial was conducted from 2022 to 2023 to examine the effects of the combined application of organic fertilizer on the growth and yield of pakchoi. Three types of irrigation water, namely fresh water (F), brackish water (B), and magnetized–ionized brackish water (MIB), were used in combination with five different organic fertilizer rates (0, 20, 40, 60, and 80 kg/ha, denoted as 0, 1, 2, 3, and 4). The results revealed that treatments F2, F3, B2, B3, and MIB3 significantly improved the growth indexes of pakchoi. Notably, treatments F3, B3, and MIB3 resulted in an earlier onset of the fast growth period for leaf area index and fresh weight. During this period, we observed the highest cumulative growing degree days (ΔCGDD) values, which were 628.36 °C for plant height (MIB4), 475.01 °C for leaf area index (B3), 259.73 °C for fresh weight (B3), and 416.82 °C for dry matter accumulation (B3). The logistic model indicated an increase in eigenvalue at an organic fertilizer application rate of 60 kg/ha, while excessive fertilization had inhibitory effects. Under brackish water irrigation, both plant height and leaf area index demonstrated significant positive effects on yield, with plant height having a particularly noteworthy direct effect at a coefficient of 0.935. MIB water irrigation demonstrated superior advantages for promoting pakchoi growth, leading to significantly higher rates of fresh weight and dry matter accumulation compared to traditional brackish water irrigation. The maximum value of each growth index exerted a significant direct influence on its respective growth parameter, whereas ΔCGDD demonstrated a relatively smaller or potentially negative effect. Applying organic fertilizer appropriately can assist in the production of pakchoi and provide a scientific basis for increasing yield.