Water-saving irrigation is of extraordinary importance for tomato production in semi-arid areas of northwest China. For this purpose, we conducted a two-season trial in a solar greenhouse of two tomato genotypes named ‘181’ and ‘Mao Fen 802’ and cultivated with substrate, under four irrigation regimes, i.e., well-watered (WW), low (LWD, 80% WW), moderate (MWD, 60% WW) and high (HWD, 40% WW) water deficit. The substrate water content of WW treatment was 75%θf to 90%θf (where θf is the field capacity). The study results showed that the single fruit weight and yield of tomato were significantly declined with an increasing water deficit degree. Compared to WW treatment, the fruit weight and yield were decreased about 34.45% and 20.35% for ‘181’ and ‘Mao Fen 802’ under HWD treatment, respectively. Conversely, water deficit treatment led to an obvious promotion of WUE and showed an upward trend as the water deficit level increased. In addition, compared to WW treatment, the water deficit significantly decreased the total flavonoids of the ‘181’ tomato by 24.4–93.1%, whereas there was no significant impact on that of ‘Mao Fen 802’. Nonetheless, different individual polyphenols were increased by suitable deficit irrigation for two tomato cultivars. Gallic acid, 3,4-dihydroxybenzoic acid, and naringin of ‘181’tomato were increased by 128.4–195.2%, 8.6–43.7%, and 31–73-fold, respectively, under water deficit compared to WW treatment. Further, under water deficit treatment, p-coumaric acid, benzoic acid, and 3,4-dihydroxybenzoic acid of ‘Mao Fen 802’ were increased by 36.2–49.2%, 59.1–189.7%, and 36.3–106.4% compared to WW treatment. As the main carotenoid component, the lycopene content of tomato fruit exhibited a significant rise of 7.84–20.02% and 20.55–32.13% for ‘181’ and ‘Mao Fen 802’ under three degrees of water deficit compared to WW treatment. Linear regression showed a significantly positive relationship between irrigation amounts and yield, and total polyphenols, whereas there was a significantly negative relationship between irrigation amounts and WUE, and total carotenoids. Based on correlation and PCA, WW and LWD, and MWD and HWD, were gathered together for ‘181’, while LWD, MWD, and HWD, were gathered, and only WW scattered for ‘Mao Fen 802’, along the PC1 direction. It was proposed that ‘Mao Fen 802’ was more sensitive to water deficit than the ‘181’ tomato. In conclusion, water deficit is conductive to water-saving cultivation of the greenhouse tomato and the tomato genotypes, and water deficit level is a key factor necessary for consideration.