Abstract: Soil samples were collected from the fields planted with alfalfa for different years in the hilly region of southern Ningxia, and the technique of synchrotron radiationfourier transform infrared spectroscopy (SR-FTIR) was adopted to study the characters of soil organic carbon (SOC) functional groups in different sizes of soil aggregates. Planting alfalfa changed the contents of SOC functional groups and their distribution in soil aggregates. With the increasing year of planting alfalfa, the SOC content, percentage of macroaggregates (>0.25 mm), aggregates stability, and relative content of SOC saturated alkyl all increased, and the saturated alkyl was mainly distributed in 0.25-1 mm aggregates. However, the relative contents of SOC aliphatic-C and alcohol-C decreased with the increase of soil aggregate size. The increased aliphatic-C and alcohol-C were mainly distributed in macro-aggregates, whereas the aromatic-C was mainly distributed in <0.25 mm aggregates. The variation range of the relative contents of the functional groups in macro-aggregates was larger than that in <0.25 mm aggregates, showing that the SOC stability in micro-aggregates was higher than that in macro-aggregates. Continuous planting of alfalfa made the increment of SOC easily oxidizable functional groups (aliphatic-C and alcohol-C) be larger than that of aromatic-C and the chemical stability of SOC increased, with the best effect observed in 8-year planting. The aliphatic-C, alcohol-C, and saturated alkyl in SOC had higher percentages, their variation was most active, and had great contribution to the increase of SOC content.