The aim of this study was to investigate the relationship between the microstructure of a CAD/CAM composite and the silanization effect on adhesive bonding, using surface free energy (SFE) analysis. Six commercial CAD/CAM composites, as well as control samples of two glass-ceramics and a resin, were investigated. The samples were characterized by morphological observations and SFE analysis. The bonding characteristics of the samples with the resin-cement were evaluated according to the silanization effect, which was determined from the ratio between the shear-bond strengths for the sample groups, with and without a silane-primer application. The composites were classified into two groups in terms of their microstructure; ENAMIC exhibits a polymer-infiltrated-ceramic-network (PICN) structure, while the other composites have a dispersed-filler (DF) structure. The dispersive component of the SFE was significantly lower in the PICN composite than in the DF composites. On the other hand, the polar component of the SFE was significantly higher in the PICN composite than in the DF composites. These SFE components were similar to those of glass-ceramics for the PICN composite and to those of the resin for the DF composites. The silanization effect increased linearly with the polar component or with a decrease in the dispersive component. Additionally, the silanization effect increased with the inorganic content. As a result, the silanization effect was found to be the highest for the PICN structure of ENAMIC. The results revealed that the silanization effect on the adhesive bonding is more effective for a PICN composite than for a DF composite.