Soil water deficit is one of the major limiting factors for crop growth in the dryland areas of China's Loess Plateau. To improve the use of hydrothermal resources by crops in this region, a three-year field experiment (2020-2022) was conducted to investigate the effects of replacing chemical fertilizers (F1: N 112.5 kg ha(-1), P 75 kg ha(-1), K 67.5 kg ha(-1); F2: N 225 kg ha(-1), P 150 kg ha(-1), K 135 kg ha(-1)) with sheep (S1: 12.5 t ha(-1); S2: 25 t ha(-1)) and chicken manure (C1: 5.8 t ha(-1); C2: 11.6 t ha(-1)) on soil hydrothermal dynamics and crop carbohydrate allocation of oilseed flax. The results revealed that the period of peak crop water demand was not synchronized with the annual rainfall distribution. The S2 treatment significantly enhanced precipitation storage efficiency (PSE) during the fallow period, increasing by 1.75-12.47 % in 2021 and 4.12-12.49 % in 2022 (P < 0.05). Moreover, while it increased total evapotranspiration (ET) by 1.58-5.12 % compared with other fertilization treatments, it optimized water allocation across growth periods, resulting in reduced ET during the critical vegetative-reproductive overlap phase. Furthermore, organic manures diminished the effective accumulation of soil temperature during high-temperature periods, curtailing soil water consumption. Averaged across the two growing seasons, the 25 t ha(-1) sheep manure treatment increased grain yield by 4.33-38.57 % and WUE by 3.00-31.09 % compared to the other treatments (P < 0.05). Organic manure effectively enhanced stress resistance by optimizing the allocation of non-structural carbohydrates (NSC), as evidenced by the S2 treatment increasing capsule starch content by 13.44-41.39 % in 2021 and 5.58-42.54 % in 2022 compared to other treatments (P < 0.05). In conclusion, for dryland cropping on the Loess Plateau, 25 t ha(-)(1) sheep manure proves to be an integrated approach that coordinates water conservation and carbon metabolism to boost productivity and stress resistance.