Crop harvesting and residue removal from croplands often result in imbalanced biogeochemical cycles of carbon and nutrients in croplands, putting forward an austere challenge to sustainable agricultural production.  As a beneficial element, silicon (Si) has multiple eco-physiological functions, which could help crops to acclimatize their unfavorable habitats.  Although many studies have reported that the application of Si can alleviate multiple abiotic and biotic stresses and increase biomass accumulation, the effects of Si on carbon immobilization and nutrients uptake into plants in croplands have not yet been explored.  This review focused on Si-associated regulation of plant carbon accumulation, lignin biosynthesis, and nutrients uptake, which are important for biogeochemical cycles of carbon and nutrients in croplands.  The tradeoff analysis indicates that the supply of bioavailable Si can enhance plant net photosynthetic rate and biomass carbon production (especially root biomass input to soil organic carbon pool), but reduce shoot lignin biosynthesis.  Besides, the application of Si could improve uptake of most nutrients under deficient conditions, but restricts excess uptake when they are supplied in surplus amounts.  Nevertheless, Si application to crops may enhance the uptake of nitrogen and iron when they are supplied in deficient to luxurious amounts, while potassium uptake enhanced by Si application is often involved in alleviating salt stress and inhibiting excess sodium uptake in plants.  More importantly, the amount of Si accumulated in plant positively correlates with nutrients release during the decay of crop biomass, but negatively correlates with straw decomposability due to the reduced lignin synthesis.  The Si-mediated plant growth and litter decomposition collectively suggest that Si cycling in croplands plays important roles in biogeochemical cycles of carbon and nutrients.  Hence, scientific Si management in croplands will be helpful for maintaining sustainable development of agriculture.