In this study, the characteristics of soil macroaggregate formation mediated by exogenous organic matter application (vermicompost and vinegar residue) in coastal saline-alkali soil were investigated through a field experiment. The results showed that adding exogenous organic matter promoted the formation of soil macroaggregates, increased fertility indicators (carbon, nitrogen and phosphorus) and decreased barrier factors (pH, electrical conductivity (EC) and salinity) of soil macroaggregates. Under the highest application rate, salinity of soil macroaggregates decreased by an average of 34.0% in vermicompost-treated soils and 46.5% in vinegar residue-treated soil. Exogenous organic matter application increased enzyme activities and significantly changed the bacterial and fungal community compositions and structures of soil macroaggregates. With the same application rate, vermicompost was more favorable for the formation of soil macroaggregates and the increase of soil fertility, while vinegar residue was more favorable for the reduction of soil salinity. Structural equation modeling showed that soil organic carbon and EC or salinity were main factors affecting macroaggregate formation, but the changes in soil fertility, enzyme activity and microbial community structure could have differential effects on macroaggregate formation.