Numerous approaches have been developed to control the crystalline and morphology of calcium carbonate. In this paper, nanobubbles were studied as a novel aid for the structure transition from vaterite to calcite. The vaterite particles turned into calcite (100%) in deionized water containing nanobubbles generated by high-speed shearing after 4 h, in comparison to a mixture of vaterite (33.6%) and calcite (66.3%) by the reaction in the deionized water in the absence of nanobubbles. The nanobubbles can coagulate with calcite based on the potential energy calculated and confirmed by the extended DLVO (Derjaguin–Landau–Verwey–Overbeek) theory. According to the nanobubble bridging capillary force, nanobubbles were identified as the binder in strengthening the coagulation between calcite and vaterite and accelerated the transformation from vaterite to calcite.