Heterostructurally engineered CdZnSeS@ZnS quantum dots (QD) materials are synthesized through surface modification involving ligand exchange, changing the surface chemistry from hydrophobicity to hydrophility. The hydrophilic characteristics of the CdZnSeS@ZnS QDs are exploited in the artificial monitoring of the cracks present in the smart composite building materials. The synthesized CdZnSeS@ZnS QDs demonstrate that the average sizes of CdZnSeS and CdZnSeS@ZnS QDs are 9.5 and 12.7 nm, respectively. The presence of ZnS shell (~1.6 nm) functions as an effective physical barrier in order to enhance the stability of QDs against environmental changes such as the ligand exchange process. The optimized CdZnSeS@ZnS QDs, exhibit high-quality fluorescent features with a peak emission wavelength of 525 nm. The current work chose the shape memory alloy(SMA)/cement composites as a model system of cement-based materials, due to its applicability to self-healing functions mediated through shape memory alloys immersed into the cementitious matrix. The SMA/cement composites are subjected to the hostile mechanical loading, leading to mechanical defects, cracks and subsequently were heated to heal cracks mechanically generated. The insertion of aqueous QD solutions to the recovered SMA/cement composites is evaluated in terms of structural health monitoring. Unlike the previous crack monitoring approaches, the water-dispersed QD materials demonstrate the facilitated infiltration to the crack networks and the effective monitoring capability with the aid of highly luminescent quantum dots. The unique features are discussed with the main emphasis on the hydrophilic properties of the CdZnSeS@ZnS QDs. The aqueous QD solution approach is proven to be suitable for monitoring complex cracks and self-healing features in smart composite materials which will be employed in buildings and infrastructures.