Background Extreme weather events are predicted to increase, such as combined heat and drought. The CO2 concentration ([CO2]) is predicted to approximately double by 2100. We aim to explore how tomato physiology, especially photosynthesis, is affected by combined heat and drought under elevated [CO2] (e [CO2]). Results Two genotypes, 'OuBei' ('OB', Solanum lycopersicum) and 'LA2093' (S. pimpinellifolium) were grown at a [CO2] (atmospheric [CO2], 400 ppm) and e [CO2] (800 ppm), respectively. The 27-days-old seedlings were treated at 1) a [CO2], 2) a [CO2] + combined stress, 3) e [CO2] and 4) e [CO2] + combined stress, followed by recovery. The P-N (net photosynthetic rate) increased at e [CO2] as compared with a [CO2] and combined stress inhibited the P-N. Combined stress decreased the F-v/F-m (maximum quantum efficiency of photosystem II) of 'OB' at e [CO2] and that of 'LA2093' in regardless of [CO2]. Genotypic difference was observed in the e [CO2] effect on the gas exchange, carbohydrate accumulation, pigment content and dry matter accumulation. Conclusions Short-term combined stress caused reversible damage on tomato while the e [CO2] alleviated the damage on photosynthesis. However, the e [CO2] cannot be always assumed have positive effects on plant growth during stress due to increased water consumption. This study provided insights into the physiological effects of e [CO2] on tomato growth under combined stress and contributed to tomato breeding and management under climate change.