The effect of groundwater salinization on the stability of soil aggregates and the organic carbon pool was explored using the soil in seasonally humid area and the perennial dry area of Bayinbuluk alpine wetland. Four levels of groundwater were used in this study including control (NaCl 0 g/L), brackish water (NaCl 2 g/L), salt water (NaCl 6 g/L), and brine water (NaCl 23 g/L). The soil aggregates were classified into different sizes by wet sieving method. Results showed that the groundwater salinization had not significant effect of soil aggregates in 0—10 cm depth, but had a significant effect on the percentage of soil aggregates in 10-30 cm depth. With the increase of salinity, the percentage of soil aggregates > 2 mm first decreased and then increased. In 10—30 cm soil cglayer, the lowest values of the percentage of soil aggregates > 2 mm with the value between 1% and 14% were found in the 2 g/L treatment, while the values (5%~56%) increased significantly in the 23 g/L treatment. The percentage of soil aggregates > 2 mm in seasonally humid area was higher than that in perennial dry area. The mean weight diameter (MWD) and geometric mean diameter (GWD) in seasonally humid area increased first and then decreased with increasing soil depth, while MWD and GMD in perennial dry area decreased with increasing soil depth. MWD and GMD in 0—10 cm depth were significantly higher than those in other soil depths, and MWD (0.71~3.59 mm) and GMD (0.25~1.64 mm) under the 23 g/L treatment in 10—30 cm depth were significantly higher than those under the other treatments. Content of aggregate associated organic carbon in 0—10 cm depth first increased and then decreased with decreasing aggregates size. Content of aggregate associated organic carbon in 20—30 cm depth had similar change trend as in the 0-10 cm depth. Contents of soil organic carbon in 2~0.25 mm soil aggregates under the 6 and 23 g/L were significantly higher than other treatments. In conclusion, the groundwater salinization had a significant effect on the soil aggregates stability and organic carbon content in the 10—30 cm depth in the seasonal humid area and the perennial area, and the groundwater salinity of 2 g/L have damage effects on soil aggregates, which reduces the stability of the soil aggregates. The salinity with the value of 23 g/L has mild protective effect on > 2 mm soil aggregate. With decrease of the aggregates size, the soil organic carbon content reduces, and the content of macro-aggregate (> 0.25 mm) associated organic carbon is higher than other soil aggregates.