Field positioning experiments with split-plot design were conducted for five consecutive years on winter wheat which was used as the test crop in the dryland of Northwest China. The main treatment was five nitrogen application rates (N 0, 75, 150, 225, 300 kg/hm²), while the secondary treatment was mixed with or without organic fertilizer (30 t/hm²). After harvesting in June 2019, we took samples of soil layers of 0—10, 10—20, and 20—40 cm to measure and analyze soil physical properties such as soil bulk density, saturated hydraulic conductivity, and water stable aggregates. The results showed that the combined application of organic and inorganic fertilizer significantly increased the winter wheat yield compared with the single application of chemical fertilizer, with an average increase of 13% in five years, and the best effect was N150+M treatment. After the application of organic fertilizer, the bulk density of the tested soil decreased. In the 0—10, 10—20, and 20—40 cm soil layers, the bulk density of treatments received organic fertilizer respectively decreased by 4%, 2%, and 4%. In the 0—10 cm soil layer, the combined application of organic and inorganic fertilizers reduced the saturated hydraulic conductivity of each treatment compared with the single application of chemical fertilizers, but failed to reach a significant difference. Compared with N0 treatment, the water-stable aggregates of >2 mm respectively increased by 224%, 105%, and 3% in the 0—10, 10—20, and 20—40 cm soil layers under N0+M treatment. The MWD and GMD values of the soil aggregates in the 0—40 cm soil layer did not change significantly when the organic and inorganic fertilizers were combined with chemical fertilizers. But the nitrogen application rate of 150 kg/hm² had a stable effect on the water-stable aggregates of the tested soil and had a certain promoting role. To sum up, the application of N 150 kg/hm² with organic fertilizer 30 t/hm² is beneficial to the increase of winter wheat yield and the stability of the soil structure in the northwest dryland.