In order to study the effect of different organic materials on the distribution of micro-aggregates in native saline soils and the adsorption capacity of different fractional micro-aggregates on organic carbon, the native saline-alkali soils were used as test objects. The field experiment included the control treatment (CK), granular straw treatment (GW), normal corn straw treatment (CS), forage treatment (GS) and sheep manure treatment (SM). Combined with laboratory analysis, the particle size distribution of soil micro-aggregates and the content of organic carbon between different size micro-aggregates were studied. The results showed that the application of organic materials increased the contents of micro-aggregates of 2~0.25 mm in soil compared with CK, with an increase of 9.02%~20.37% and an order of GW > SM > GS > CS > CK. There were some differences in the effects on the micro-aggregates with other particle sizes. In general, organic material application increased the large particle size soil micro-aggregates and reduced the soil micro-aggregates with small particle size. The application of different organic materials could increase the organic carbon content of soil micro-aggregates of various particle sizes. At the same time, the application of organic materials increased the stability of soil micro-aggregates. The regression model analysis, correlation analysis and redundant analysis and principal component analysis were used for factor analysis. The results showed that the application of granular straw was more beneficial to increase the stability of soil microaggregates.