This study aimed to investigate the possibility that a calcium phosphate ion cluster (CPIC)-incorporating phosphoric acid (PA) solution promotes the remineralization of the hybrid layer and prevents nanoleakage from the dentin–resin interface, thereby minimizing dentin–resin bond failure during long-term bonding periods. The specimens were prepared using human molars and treated with three types of etching solutions (35% PA, and CPIC-incorporated PA solutions at 1:1 and 1:2 ratios). The microtensile bond strength (µTBS) of half of the specimens was measured after 24 h, and measured after thermocycling for the other half. Fourier-transform infrared spectroscopy (FTIR) was performed to chemically analyze the remineralization, and the degree of nanoleakage in each sample was observed using a scanning electron microscope (SEM). The CPIC-incorporated PA-II solution decreased the nanoleakage in the hybrid layer without reducing the µTBS, with or without thermocycling, and promoted remineralization of dentin collagen.