Advancements in micropropagation techniques facilitated the incorporation of nanoparticles in the propagation of many commercially important plants. Under in vitro conditions, the adventitious shoots are regenerated with undesirable structural disorders, which increase the rate of mortality of in vitro-produced propagules. In the present study, the effect of Silicon nanoparticles (SiNPs) along with the optimized plant growth regulators (PGRs) in the nutrient medium were tested for their growth-promoting effects on in vitro developing shoots of Cyperus rotundus L. Silicon NPs at 5.0 mg/L induced a higher number of shoots (23 shoots/culture vessel) with improved shoot morphology, rhizogenesis (7.0 roots with 4.0 cm root length), photopigments [(chl a - 474.0 μg/g fresh weight (FW); chl b- 509.0 μg/g FW)] and biomass (3.0 g FW), which were comparatively superior to the morphometric outcomes of the control experiments. The occurrence of morphometric and anatomical disorders in the leaves such as non-functional stomata with increased stomatal density, underdeveloped epidermal cells, undifferentiated costal and intercostal regions, and reduced mesophyll, sclerenchyma, xylem vessels, and phloem elements was observed in the controlled shoots. Silicon NPs at 5.0 mg/L in the medium reduced the in vitro-induced structural abnormalities and modulated foliar micro-morpho-structural differentiation of leaves by promoting positive structural alterations in the leaf thickness, differentiation of dermal tissues, Kranz anatomy, vascularization, stomatal complex, and mechanical tissues. These overall developmentssupported the hardening and survival of plantlets ex vitro. The present findings report the role of SiNPs as the ‘structural stabilizer’ during in vitro plantlet development of C. rotundus, as a target species and representative model for the C4 plants.