Layered fertilization parameters affects crop root system configuration and growth distribution, which in turn affects soil pore properties and aggregate structure. Therefore, understanding the spatial distribution of the root system and soil pore space is helpful in choosing a reasonable fertilization ratio in production practice, which ensures high and stable crop yields and at the same time improves fertilizer utilization and soil health. Albeit the impact of layered fertilization ratio at varied rates on soil pore characteristics in the soil profile at a microscale level remains limited. This study quantifies the impacts of layered fertilization ratio under on rapeseed root distribution and soil pore characteristics using the root analysis system and X-ray computed tomography (XCT). A new fertilization pattern that shallow-deep layer synchronized mechanical sowing was using, rotary tillage mixed fertilization in the shallow layer and 10 cm side-deep band fertilization in the deeper layer. It set five ratios of fertilizer amounts between shallow and deep layers as 0:4 (FD), 1:3 (FL), 2:2 (FM), 3:1 (FH), and 4:0 (F0), with non-fertilization (CK) as the control treatment. The results indicated that layered fertilization effectively improved the rape root conformation and spatial distribution, significantly increased total soil porosity and moisture content, and reduced soil bulk density and resistance (
P
< 0.05). Additionally, root configuration is closely related to soil pore structure and crop yield. Notably, compared with other treatments, the macroscopic porosity, equivalent pore diameter, hydraulic radius and roundness of FM treatment are significantly improved, and it effectively improves the yield and quality of rapeseed. Correlation analysis showed that the root system configuration parameters were negatively correlated with soil bulk density and resistance but positively correlated with soil moisture content, and macropore morphology parameters and rapeseed yield. Our study demonstrate that layered fertilization can improved rape growth and soil macropore porosity, but its effect depends on good tillage macropore characteristics and distribution created by reasonable fertilization ratio, which provided a theoretical basis for high-yield, efficient, green, and sustainable mechanized direct-sowing production of rapeseed.