Effect of elevated atmospheric CO2 (e[CO2]) on plant growth and physiology depends on soil nutrient availability. The objective of this study was to evaluate the effect of e[CO2] impact on tobacco (Nicotiana tabacum L.) growth and physiology, and to test if patchy root-zone nutrient supply could modulate the e[CO2] effects on tobacco crops. In this study, we investigated how partial root-zone nutrient deficiency (PRN) affect carbon assimilation, biomass accumulation and partitioning, and water use efficiency (WUE) of tobacco grown under e[CO2]. A split-pot experiment was conducted with tobacco plants grown in a sandy loam soil with two fertilizer levels [0 and 113-68-258 (N-P2O5-K2O) mg kg−1 soil] and three fertilization regimes (PRN, full root-zone fertilization – CRN, and no fertilization – CK) and two CO2 environments (400 μmol L−1 and 800 μmol L−1). Compared with ambient [CO2] (a[CO2]), e[CO2] increased the leaf photosynthetic rate (Pn) and reduced the transpiration rate (Tr) and stomatal conductance (gs), resulting in an increased WUE. Besides, e[CO2] enhanced tobacco leaf biomass and partitioning towards roots compared with a[CO2]. Improved growth under e[CO2] compared with a[CO2] was more pronounced under PRN than under CRN. Root hydraulic conductance was significantly greater under PRN as compared with other fertilization regimes particularly under e[CO2]. Root exudates of glucose and sucrose were significantly improved by the interaction of [CO2] and patchy fertilization regime, especially after 7 days exposure to different CO2 growth conditions. The soil pH was unaffected by CO2 growth environment but was significantly lowered in the fertilized side under PRN as compared to other fertilization regimes. Collectively, our results offer novel information about the modulation of e[CO2] on the physiology and growth of tobacco plants under patchy soil nutrient deficiency.