In this study, 3-aminopropyltriethoxysilane (KH550) and vinyltrimethoxysilane (KH171) were used to modify aggregates and prepare aggregates with different surface wettability. The effect of silane coupling agents on aggregate surface properties was characterized through FT-IR, XPS, contact angles and aggregate water absorption. The influence of the aggregate’s surface wettability on the interface properties was discussed using MIP, SEM, BSE and nanoindentation, and then the influence mechanism of the interface microscopic properties on the macro-properties of mortar was revealed. The results showed that the type of silane has an intense impact on the surface properties of aggregates. KH550-modified aggregates increased the contact angle from 23.6° to 59°, while KH171-modified aggregates increased it from 23.6° to 91.6°. Silane-modified aggregates reduced the surface hydrophilicity, thereby reducing the water absorption and improving the mortar’s workability. However, KH550-modified aggregates exhibited a more effective enhancement of the mortar’s mechanical properties. Specifically, KH550-modified aggregates reduced the aggregate’s surface hydrophilicity, consequently alleviating the interfacial edge effect. This led to a 10% increase in the compressive strength of the mortar, an 11.6% reduction in the porosity, an 8.4% decrease in the interfacial porosity, and a 42.3% increase in the elastic modulus of the ITZ. Meanwhile, the cement matrix obtained a greater amount of water for cement hydration, resulting in an increased degree of hydration and an 18.5% increase in the elastic modulus of the cement matrix. The improvement in the ITZ between the modified aggregates and the cement matrix is considered to be one of the fundamental reasons for the enhancement of the mortar’s performance.