The influence of biochar on the soil structure and aggregate stability has been debated in previous studies. To probe the action of biochar on soil aggregates, a 5-year field experiment was implemented in the brown earth soil of northeastern China. We determined the aggregate distribution (> 2000 μm, 250–2000 μm, 53–250 μm, and < 53 μm) and organic carbon (OC) and organo-mineral complex contents both in the topsoil (0–20 cm) and within the soil aggregates. Three treatments were studied as follows: control (basal application of mineral NPK fertilizer), biochar (biochar applied at a rate of 2.625 t ha−1), and stover (maize stover applied at a rate of 7.5 t ha−1), and all treatments received the same fertilization. The biochar and stover applications decreased the soil bulk and particle densities significantly (p < 0.05) and enhanced the soil total porosity. Both amendments significantly (p < 0.05) enhanced the total OC, heavy OC fractions, and organo-mineral complex quantities in the bulk soil as well as in all the studied aggregate fractions. Biochar and stover applications promoted the formation of small macroaggregates. A greater amount of organic matter was contained in the macroaggregates, which led to the formation of more organo-mineral complexes, thereby improving soil aggregate stability. However, the different mechanisms underlying the effect of biochar and stover on organo-mineral complexes need further research. Biochar and stover applications are both effective methods of improving the soil structure in Northeast China.