Soil organic carbon (SOC) accumulation plays an important role for achieving the goals of Paris Agreement. Biochar has a negative or positive effects on SOC accumulation, which is related to soil aggregate fractions and structural characteristics of SOC. In this context, however, the information about the long-term effects of biochar application on SOC accumulation under field conditions was scarce. The changes of SOC and its functional groups in bulk soil, aggregate stability, and the distribution of SOC in aggregate fractions were evaluated by means of 8 years’ field experiment, in which biochar (derived from apple branches pyrolyzed at 550 °C) was applied into soil at the rates of 1% (B1), 3% (B3), and 5% (B5) (w/w), and took the soil without biochar application as the control treatment (CK). Compared with CK, B3 and B5 increased the > 250-μm fraction (macroaggregate) and decreased the < 53-μm fraction and ultimately increased the aggregate stability by 16.9% and 35.3%, respectively. The B3 and B5 significantly increased the SOC in all aggregate fractions. However, B1 had no significant effects on soil aggregate fractions and the associated C. For macro- and micro-aggregates, the aromatic-C was higher and polysaccharide-C was lower in B3 and B5 than in CK, while these were opposite in B1. Compared with the first year, the SOC in the eighth year under CK and B1 was decreased by 0.47 and 3.36 g kg−1 respectively, while the one under B3 and B5 was increased by 1.55 and 7.59 g kg−1, respectively. The long-term application of biochar with 3% and 5% rates (but not 1% rate) is conducive to the accumulation of SOC of clay loam soil, which is further beneficial to enhance the soil carbon pool stability.