Elevated CO2 concentration (e[CO2]) could induce the decline of nutrient concentration in tomato fruit, although it enhances the yield. Alternate partial root drying (PRD) irrigation is a water-saving irrigation strategy, which may enhance tomato fruit quality including both organic and inorganic attributes. Yet, it remains unknown whether PRD could alleviate the negative impact of e[CO2] on the quality attributes of tomato fruit. To investigate that, two genotypes of tomato plants differing in their endogenous abscisic acid level, i.e. Ailsa Craig (wild type, WT) and its correspondent ABA-deficient mutant (flacca), were grown in ambient CO2 (a[CO2], 400 ppm) and e[CO2] (800 ppm) environment, respectively. And three irrigation regimes including full irrigation (FI), deficit irrigation (DI) and PRD were applied during anthesis to fruit ripping stages. The results showed that e[CO2] increased net photosynthetic rate, decreased stomatal conductance and transpiration rate. Tomato yield was more sensitive to irrigation regimes than [CO2], and the reduction of fruit yield caused by PRD was attenuated under e[CO2], especially in flacca. Both e[CO2] and PRD enhanced water use efficiency. The concentration of total soluble solid, total sugar and total acid, as well as fruit firmness were improved in PRD. A negative effect of e[CO2] on fruit mineral nutrition was seen only in flacca, and as expected, such impact was attenuated by the reduced irrigation regimes (DI and PRD). Collectively, it is suggested that the responses of tomato fruit quality to e[CO2] and reduced irrigation regimes are genotypic-dependent, where the endogenous ABA level of the plants plays an important role, and this must be considered in climate management in greenhouse tomato cultivation.