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Heliogreenhouse has become the major protected horticulture industry in China due to its environmental friendly and energy saving features, however, the healthy development of heliogreenhouse is still limited by many problems. In view of extremely CO2 deficient and water resources waste caused by lax water management in heliogreenhouse, we investigated the growth and photosynthetic characteristics of tomato plants under four different CO2 levels, i.e., ambient CO2 concentration in heliogreenhouse (about 450μmol/mol), elevated CO2 concentrations are (700±50)μmol/mol (low), (1000±50)μmol/mol (moderate), (1300±50)μmol/mol (high) combined with three different water levels, i.e., substrate water content are 35%~45% (low), 55%~65% (moderate), 75%~85% (high) of saturated substrate water content. The results showed that biomass of below ground, net photosynthetic rate, chlorophyll contents (SPAD) were increased and plants bloomed 6~11 d earlier in moderate and high CO2 level plants. AQY and ACE were markedly increased by 45%~118% and 66%~81%, respectively; meanwhile, LCP was significantly reduced by 34%~57% in CO2 enrichment plants under moderate water condition. Compared with low water level, Pmax was markedly increased by 42.8% and 52.1%; AQY was markedly increased by 10.7% and 25.9%; LCP was reduced by 29.1% and 63.4%; CCP was reduced by 20.8% and 8.3% in moderate and high water level plants under the measured high CO2 condition, respectively. Compared with the plants grown under ambient CO2 concentration, the MDA content reduced by 4%~10% in CO2 elevated plants under low water condition, this indicated that CO2 enrichment could alleviate oxidative damage of tomato plants that subjected to low water condition. Compared with the plants that grown in moderate water level under ambient CO2 concentration, blooming time was 3~7 d earlier and yield of first spike fruit was increased by 18%~44% in low water level plants under CO2 elevated conditions, meanwhile, compared with the plants that grown in high water level under ambient CO2 concentration, blooming time was 8 and 10 d earlier and yield of first spike fruit was increased by 42.8% and 34.0% in moderate water level plants under moderate and high CO2 condition, respectively, this indicated that water use efficiency which related to yield was enhanced by elevating CO2 concentration.