This case takes citrus garden in purple hilly area as the research object, using mechanical deep loosening method, according to the number of ditch irrigation biogas fertilizer (one subsoiling ditch nitrogen 45 t/hm2 biogas fertilizer), we research the effects of biogas fertilizer deep application in citrus orchards soil aggregates, soil nutrient and yield of Citrus, we set 5 pieces of experiment treatment: (1) CK:only fertilizer application; (2) T0: no subsoiling + biogas fertilizer 45 t/hm2; (3) T2:2 subsoiling + biogas fertilizer 135 t/hm2; (4) T3:3 subsoiling + biogas fertilizer 180 t/hm2, (5) T5:5 subsoiling + biogas fertilizer 270 t/hm2. Results show that: Biogas fertilizer improves the number of soil in 0.25～2 mm water stable aggregates, reduces the ＜0.25 mm microaggregate number and 2～5 mm water stable aggregate amount significantly increased with increase of subsoiling ditch and biogas fertilizer application amount; In the 0-20 cm soil layer T3 and T5 treatment aggregate mean weight diameter (MWD) respectively, compared to the control treatment and biogas fertilizer without T0 treatment improves the 27.6%～29.9% and 12.2%～14.2%.The content of organic matter, total nitrogen and total phosphorus in 20 cm soil layer was higher than that of 20—40 cm and 40—60 cm. In 0—20 cm soil layer, soil organic matter content of the T3 treatment were increased 1.46～2.90 g/kg and 5.00～6.44 g/kg compared with the soil organic matter content of CK and T0. The biogas fertilizer deep application of T5 treatment significantly increased the contents of soil total nitrogen content. T3 and T5 treatment can significantly improve the total phosphorus content of 0—20 cm and 20—40 cm and total potassium content of 20—40 cm soil. Compared with conventional fertilization (CK), T3 and T5 treatment significantly improved the yield of Citrus in the test orchard, and the average yield were 3.57 and 3.66×104 kg/hm2 in 2014—2015, the average yield increased 4.20% and 7.02%; Each biogas fertilizer (T0、T2、T3、T5) is significantly higher than the solid acid of CK, the ratio of solid acid level of performance are T3＞T5＞T2＞T0＞CK; T5 treatment significantly increased the content of Vc, two years were increased 4.39 and 4.48 g/100ml respectively. Hilly orchard rows deep application biogas fertilizer (180～270 t/hm2) not only can improve soil structure as well as the nutrient content, and improve the yield and fruit quality for 2 years, so that it can ensure the sustainable development of citrus production. The results provide a scientific basis for improving soil fertility and fruit yield, orchard fertilizer rational management.