Addition method of silane coupling agent (SCA) to improve the water absorption and mechanical strength of silica particle-filled epoxy resin was investigated. Two addition methods were compared, a pre-treatment method and an integral blend method in which all components were mixed simultaneously. Bonding, hydrocarbon and fluorocarbon type SCAs were employed. The bonding type has glycidoxy or amino groups that react with epoxy resin, whereas the other types have only hydrophobic chains. The silica particle-content was in the range from 10 to 50 wt%. The integral blend method was determined to be superior to the pre-treatment method for both water absorption and mechanical strength, which was contrary to the conventional view. The effect of water absorption was consequently lowered in the order of hydrocarbon > bonding types. The fluorocarbon type SCA was also effective at low silica content. Modification of the epoxy phase by SCA addition was clarified to have a more dominant effect than the adhesion of silica/epoxy interface for the lowering of water absorption, whereas it had been conventionally considered that interfacial adhesion had a more dominant effect. The mechanical strength was higher for the bonding type than the other type.