To address the severe challenges posed by soil structure degradation and nutrient loss to the ecological environment and food safety, while achieving high-value utilization of biogas slurry waste, this study explores the effects of biogas fertilizer application concentration and method on soil physical and chemical properties and soybean yield at a depth of 0-80 cm in a greenhouse cultivation setting. The biogas fertilizer application methods and concentration combinations include: applying organic fertilizer alone (TK1), applying high-concentration biogas slurry as base fertilizer combined with organic fertilizer as top dressing (TK2), applying high-concentration biogas slurry alone (TK3), applying biogas residue as base fertilizer combined with low-concentration biogas slurry as top dressing (TK4), applying biogas residue as base fertilizer combined with organic fertilizer as top dressing (TK5), and mixing biogas residue/organic fertilizer as base fertilizer combined with low-concentration biogas slurry as top dressing (TK6), with a blank control group (CK) as the reference. The results show that compared to the control group, the application of biogas fertilizers effectively increases soil nutrient content, including total nitrogen, total potassium, alkaline hydrolyzable nitrogen, available phosphorus, and available potassium. The treatment with the highest increase in alkaline hydrolyzable nitrogen and available phosphorus in the topsoil was TK6, with an increase of 3.56 and 2.44 times, respectively. The treatment with the highest increase in available potassium in the topsoil was TK3, with an increase of 9.37 times. In the deeper soil layers, the application of high-concentration biogas slurry leads to greater downward migration of total nitrogen and total potassium, while low-concentration biogas slurry causes more downward migration of total phosphorus. On the other hand, soil aggregate structure is significantly affected by different fertilization treatments. The TK1 treatment significantly increased the number of small aggregates in the soil by 25.2%, while the TK3 treatment increased the number of medium and large aggregates by 1.68%. Compared to other treatments, the TK1 treatment resulted in the greatest nitrogen loss from the soil and the lowest soybean yield, while the TK4 treatment resulted in the highest soybean yield, approximately 290 kg/acre. In summary, applying high-concentration biogas slurry leads to the greatest increase in nutrient content in the topsoil, but these nutrients are more easily leached downward. Low-concentration biogas slurry as top dressing is more beneficial for increasing soybean yield. These findings provide theoretical and research foundations for soil improvement and the high-value utilization of biogas slurry resources.