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The combination of chemical fertilizer and biochar is regarded as a useful soil supplement for improving the properties of soil and crop yields, and this study describes how the biochar of maize straw can be used to improve the quality of the degraded black soil. This has been achieved by examining the effects of combining different amounts of biochar with chemical fertilizer on the porosities and aggregate formation of soil and exploring how these changes positively impact on crop yields. A field trial design combining different amounts of maize straw biochar [0 (NPK), 15.75 (BC1), 31.5 (BC2), and 47.25 t ha−1 (BC3)] with a chemical fertilizer (NPK) has been used to investigate changes in the formation of soil aggregate, clay content, soil organic carbon (SOC), and crop yields in Chinese black soil over a three year period from 2013 to 2015. The results of this study show that the addition of fertilizer and biochar in 2013 to black soil results in an increased soybean and maize yields from 2013 to 2015 for all the treatments, with BC1/BC2 affording improved crop yields in 2015, while BC3 gave a lower soybean yield in 2015. Total porosities and pore volumes were increased for BC1 and BC2 treatments but relatively decreased for BC3, which could be attributed to increased soil capillary caused by the presence of higher numbers of fine soil particles. The addition of biochar had a positive influence on the numbers and mean weight diameters (MWD) of soil macroaggregates (>0.25 mm) that were present, with the ratio of SOC to TN in soil macroaggregates found to be greater than in the microaggregates. The most significant amount of carbon present in macroaggregates (>2 mm and 0.25–2 mm) was observed when BC2 was applied as a soil additive. Increasing the levels of maze straw biochar to 47.25 t ha−1 led to an increase in the total organic carbon of soil, however, the overall amount of macroaggregates and MWD were decreased, which is possibly due to localized changes in microbial habitat. The supplementation of biochar increased in the amount of aromatic C present (most significant effect observed for BC2), with the ratio of aliphatic C to aromatic C found to be enhanced due to a relative reduction in the aliphatic C content with >2 mm particle fraction. These changes in organic carbon content and soil stability were analyzed using univariate quadratic equations to explain the relationship between the type of functional groups (polysaccharide C, aliphatic C, aromatic C, aliphatic C/aromatic C) present in the soil aggregates and their MWDs, which were found to vary significantly. Overall, the results of this study indicate that the use of controlled amounts of maize-straw biochar in black soil is beneficial for improving crop yields and levels of soil aggregation, however, the use of excessive amounts of biochar results in unfavorable aggregate formation which negatively impacts the yields of crop growth. The data produced suggest that aromatic C content can be used as a single independent variable to characterize the stability of soil aggregate when biochar/fertilizer mixtures are used as soil additives to boost growth yields. Analysis of soil and crop performance in black soil revealed that the application of maize-straw biochar at a rate of 15.75 and 31.5 t ha−1 had positive effects on crop yields, soil aggregation and accumulation of aromatic C in the aggregate fractions when a soybean-maize rotation system was followed over three years.