Ternary clay-based composite material (TCC), composed of lime, clay and sand, and usually modified with sticky rice and other organic compounds as additives, was widely used historically in Chinese construction and buildings due to its high mechanical performance. In this study, to gain an insight into the micromechanical mechanism of this cementitious material, the nanomechanical properties and volume fraction of mechanically different phases of the binder matrix are derived from the analysis of grid nanoindentation tests. Results show that there are five distinct mechanical phases, where the calcium silicate hydrate (C-S-H) and geopolymer present in the binder matrix are almost identical to those produced in ordinary Portland cement (OPC) and alkali-activated fly-ash geopolymer materials in nano-mechanical performance. The nano-mechanical behavior of calcite produced by the carbonation of lime in this binder is close to the calcite porous outer part of some sea urchin shells. Compared to OPC, the C-S-H contained in the TCC has a relatively lower ratio of indentation modulus to indentation hardness, implying a relatively lower resistance to material fracture. However, the geopolymer and calcite, at nearly the same volume content as the C-S-H, help to enhance the strength and durability of the TCC by their higher energy resistance capacity or higher strength compared to the C-S-H. Rediscovering of TCC offers a potential way to improve modern concrete’s strength and durability through synergy of multi-binders and the addition of organic materials if TCC can be advanced in terms of its workability and hardening rate.