Currently, it is still a tough task for dentists to remineralize dentine in deep caries. The aim of this study was to remineralize demineralized dentine in a tooth model of deep caries using nanocomplexes of carboxymethyl chitosan/amorphous calcium phosphate (CMC/ACP) based on mimicking the stabilizing effect of dentine matrix protein 1 (DMP1) on ACP in the biomineralization of dentine. The experimental results indicate that CMC can stabilize ACP to form nanocomplexes of CMC/ACP, which is able to be processed into scaffolds by lyophilization. In the single-layer collagen model, ACP nanoparticles are released from scaffolds of CMC/ACP nanocomplexes dissolved and then infiltrate into collagen fibrils via the gap zones (40 nm) to accomplish intrafibrillar mineralization of collagen. With this method, the completely demineralized dentine was partially remineralized in the tooth mode. This is a bottom-up remineralizing strategy based on non-classical crystallization theory. Since nanocomplexes of CMC/ACP show a promising effect of remineralization on demineralized dentine via biomimetic strategy, thereby preserving dentinal tissue to the maximum extent possible, it would be a potential indirect pulp capping (IPC) material for the management of deep caries during vital pulp therapy based on the concept of minimally invasive dentistry (MID).