The biotoxicity and environmental applications of carbon nanomaterials have always been the focus of research. In this research, functional carbon nanodots (FCNs) show high promotion effects on regulating the growth, development and yield of tomato under drought stress, due to their up-regulation effects on the physiological processes of plants including photosynthesis, antioxidant system, osmotic adjustment, as well as soil amelioration in physicochemical properties and microbial environment during vegetative and reproductive growth stage. The reduction of tissue water content and water use efficiency are moderated by FCNs through improving root vigor and osmolytes (soluble sugar and proline) level, which contributes to maintain the enzyme function, photosynthesis and nutrient uptake in plant. FCNs regulate the enzymatic and non-enzymatic antioxidant system to scavenge reactive oxygen species (ROS) and inhibit the lipid peroxidation, thus protect the membrane structure and function of plant cells under stress. FCNs up-regulate soil microbial communities under drought stress by regulating the soil pH, enzyme activity, organic carbon and organic matters contents. Our results prove that FCNs are biological friendly to plant growth and soil environment under drought stress, thus exhibit potential as emendator to promote plant tolerance and improve agricultural productivity in water-deficient areas.