[Objectives] To study the effects of bioorganic fertilizer application on soil physical properties and microbial biomass carbon and nitrogen in different soil layers, in order to provide scientific data for applying bioorganic fertilizer in soil improvement, soil and water conservation and the sustainable development of agricultural facilities.[Methods] Field soil tests were conducted to study the effects of bioorganic fertilizers on soil hydraulic properties, aggregate and microbial biomass carbon and nitrogen in 0-15 and 15-30 cm soil layers of fluvoaquic soil. The application rates of bioorganic fertilizer were 0, 10 and 20 t/hm², respectively.[Results] The application of bio-organic fertilizer could significantly reduce soil bulk density, increase soil porosity and hydraulics indexes. The soil bulk density decreased by 10.37%~19.26%, the field capacity and saturated hydraulic conductivity increased by 13.12%~32.25% and 37.28%~67.11%, respectively. Bioorganic fertilizer could also increase the content and average mass diameter of soil aggregates and reduce the fractal dimension of aggregates. Application of bio-organic fertilizer could increase the content of soil microbial biomass carbon and nitrogen by 33.66%~52.67% and 11.52%~22.64%, respectively. Soil physical properties had a significant correlation with microbial biomass carbon and nitrogen.[Conclusions] Application of bioorganic fertilizer can effectively improve the structure and hydraulic characteristics of fluvoaquic soil, increase the capacities of soil water storage, improve soil aggregate content, stability and microbial biomass carbon and nitrogen content.