Abstract: Water and fertilizer inputs can dominate the soil quality and crop yield during cultivation in Southwest China. It is essential to explore efficient, collaborative modes in sustainable agriculture. This study aims to systematically evaluated the diverse effects of different irrigation-fertilization modes on the soil water storage, available nutrient content, photosynthesis, edible rose yield, and irrigation water use efficiency (IWUE). A fully factorial design was established, consisting of three irrigation regimes—full irrigation (FI, 100% ETc), light deficit irrigation (DIL, 80% ETc), and moderate deficit irrigation (DIM, 60% ETc)—and four levels of organic fertilizer substitution for chemical fertilizer—R₀ (0%), R₁ (15%), R₂ (30%), and R3 (45%). The treatment FI combined with R₀ served as the control (CK). Correlation analysis and structural equation modeling were applied to explore yield-increasing mechanisms triggered by deficit irrigation with organic fertilizer partial substitution. Experimental results demonstrated that deficit irrigation strategies (DIL and DIM treatments) significantly increased the storage of available soil nutrient reserves by a margin ranging from 6.07% to 15.99%, compared with the full irrigation. Furthermore, the deficit irrigation enhanced the IWUE by 22.76% to 45.00%. The water deficit also caused a measurable decrease in essential physiological indicators. Net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), and intercellular CO₂ concentration (Ci) were reduced between 10.89% and 40.28%. The DIL treatment achieved an average increase in overall rose yield of 2.23%, with an increase in the total economic benefits of 31.25% during 2023, compared directly to the FI baseline treatment. Conversely, the DIM treatment was reduced the total crop yield and economic benefits over the consecutive two-year period, with the average 7.72% and 24.89%, respectively. Furthermore, the critical parameters—including Pn, Tr, Gs, Ci, harvested crop yield, IWUE, and overall economic benefits—exhibited initially a steady increase, followed by the decrease, as the proportion of organic fertilizer increased progressively. Absolute optimal peak values reached at the R₂ treatment level. Compared with the baseline R₀ treatment, the R₂ treatment shared a remarkable increase in the available reserves of soil nutrient, with the crop yield by 9.64% to 121.56% and 23.72% to 38.52%, respectively, after harvest. Additionally, the IWUE was also enhanced by 32.28% after treatment. The DIMR0 treatment also showed the lowest overall yield, compared with the CK. In contrast, the optimal DILR₂ treatment significantly increased the storage capacity of soil available nutrients, final crop yield, the IWUE, and the highest overall economic benefits. In addition, the structural equation model confirmed that the optimal combination of irrigation and fertilization indirectly regulated the final yield of cultivated edible roses, significantly affecting soil moisture dynamics, nutrient content, and photosynthetic parameters. This finding can provide a highly reliable reference to optimize the irrigation-fertilization systems for edible roses.