To explore effects of ecosystems on molecular structure of humus (HS) in soil aggregates, soil samples were collected from plots of grass land(GL), cultivated land(CL), and bare land(BL) in a long-term (24 years) field experiment in the black soil region of Northeast China for fractionation of soil aggregates into four particle-size fractions (>2 mm, 2～0.25 mm, 0.25～0.053 mm and <0.053 mm ) with the wet sieving method and further for analysis of structural properties of humic acid (HA) in aggregates with element analysis, infrared spectroscopy (FTIR) and differential thermal analysis (DTA) methods. Results show that the type of an ecosystem has some effects on affects molecular structure of the HA in soil aggregates. The HA in soil aggregates from CL was higher that from GL in O+S content and (O S)/C ratio, which indicates that the HA in soil aggregates from CL is higher than that from GL in oxidation degree. The DTA analysis reveals that the HA in soil aggregates from CL and BL was lower than that from GL in thermal discharge under moderate temperature, but higher in high to moderate heat ratio, suggesting that the former is higher than the latter in aromaticity/aliphaticity ratio. The HA in soil aggregates from GL and CL displays higher peaks than that from BL did at 2 920 and 2 850 cm^-1, representing C-H stretching vibration of asymmetric and symmetric aliphatic (CH₃ and CH₂), and the former was also higher than the latter in aliphatic-C/carboxylic-C(2 920/1 720) and aliphatic-C/aromatic-C(2 920/1 620) ratios. Compared with GL, the ecosystems of CL and BL both increased condensation, oxidation and aromaticity of HA in soil aggregates, thus enhancing stability of the molecular structure of HA in soil aggregates.