Fully understanding the environmental implications of engineered nanomaterials is crucial for their safe and sustainable use. Cyanobacteria, as the pioneers of the planet earth, play important roles in global carbon and nitrogen cycling. Here, we evaluated the biological effects of molybdenum disulfide (MoS₂) nanosheets on a N₂-fixation cyanobacteria (Nostoc sphaeroides) by monitoring growth and metabolome changes. MoS₂ nanosheets did not exert overt toxicity to Nostoc at the tested doses (0.1 and 1 mg/L). On the contrary, the intrinsic enzyme-like activities and semiconducting properties of MoS₂ nanosheets promoted the metabolic processes of Nostoc, including enhancing CO₂-fixation-related Calvin cycle metabolic pathway. Meanwhile, MoS₂ boosted the production of a range of biochemicals, including sugars, fatty acids, amino acids, and other valuable end products. The altered carbon metabolism subsequently drove proportional changes in nitrogen metabolism in Nostoc. These intracellular metabolic changes could potentially alter global C and N cycles. The findings of this study shed light on the nature and underlying mechanisms of bio-nanoparticle interactions, and offer the prospect of utilization bio-nanomaterials for efficient CO₂ sequestration and sustainable biochemical production.