The present study investigates the combined influence of nano-ground quartz sand, microsilica, and a polycarboxylate-based modifier on phase evolution, microstructure development, and mechanical properties in low-clinker cement systems. The main objective is to evaluate whether finely dispersed quartz acts as an inert filler or contributes to hydration processes, and to determine the critical clinker threshold governing system performance. A hybrid modifier composed of microsilica and polycarboxylate (4:1) was introduced into a clinker–gypsum system together with varying amounts of nano-ground quartz sand. The mixtures were subjected to mechanical activation in a ball mill. Chemical composition, phase evolution, and microstructure were analyzed using XRF, XRD, and TEM, while mechanical properties were evaluated through standard tests. The results show that grinding duration and modifier dosage significantly influence particle dispersion and water demand. Optimal performance was achieved at 90 minutes of grinding and 6% modifier content. A nonlinear relationship between quartz content and compressive strength was observed, with a maximum value of 57.1 MPa obtained at 30% quartz and 55% clinker content. XRD analysis confirmed partial portlandite consumption and the formation of additional low-crystalline C–S–H gel, indicating a synergistic interaction between nano-quartz and microsilica. The results demonstrate that nano-ground quartz acts not only as a filler but also as a nucleation-active component with limited pozzolanic contribution. A further reduction in clinker content below 55% leads to insufficient formation of hydration products and a decline in mechanical performance, confirming the existence of a critical clinker threshold. These results provide a scientific basis for the design of low-clinker, low-carbon cementitious materials with enhanced performance.