The effects of application concentration of biogas fertilizer and method of combined application on the physicochemical properties of soil and the soybean yield at a depth of 0-80 cm were studied under greenhouse cultivation with biogas slurry as liquid fertilizer，biogas residue and organic fertilizer as solid fertilizer，and soybean as tested crop to address the severe challenges posed by the damage of soil structure and nutrient loss to the ecological environment and food safety，while achieving the high-value utilization of waste resources from biogas slurry. The combined application methods and concentration combinations of biogas manure included organic fertilizer alone （TK1），dry fermentation biogas slurry as basal fertilizer combined with organic fertilizer as topdressing （TK2），dry fermentation biogas slurry alone （TK3），biogas residue as basal fertilizer combined with wet fermentation biogas slurry as topdressing （TK4），biogas residue as basal fertilizer combined with organic fertilizer as topdressing （TK5） and biodigne/organic fertilizer mixed base fertilizer combined with wet fermentation biogas slurry as topdressing （TK6）. The original soil （campus green soil） was set as the blank control group （CK）. The results showed that TK6 had the highest increase in the content of alkaline nitrogen and available phosphorus in the tillage layer of soil，which increased by 3.56 and 2.44 times，respectively. TK3 had the highest increase in the content of available potassium in the tillage layer of soil，with an increase of 9.37 times. The content of total nitrogen and total potassium in the dry fermentation biogas slurry were easy to migrate downward at a depth of 60-80 cm in soil，and the content of total phosphorus in the wet fermentation biogas slurry was easy to migrate downward at a depth of 80 cm in soil. The structure of soil aggregates was significantly affected by the treatment of fertilization. TK1 significantly increased the number of small soil aggregates by 25.2%. TK3 increased the number of large and medium aggregates in soil by 1.68%. Compared with other treatments，the TK1 had the highest loss of nitrogen in soil and the lowest yield of soybeans，while TK4 had the highest yield of soybeans about 4 350 kg/hm². It is indicated that the application of dry fermented biogas slurry alone significantly increases the content of nutrients in the tillage layer of soil and makes it easier for nutrients to migrate downwards. The combination of biogas residue as base fertilizer and wet fermented biogas slurry as topdressing is more conducive to improving the yield of soybeans.