Quantitative analysis of tomato root water uptake and soil water utilization in the root zone under deficit irrigation is an important tool to improve agricultural water utilization efficiency. In this study, three different deficit irrigation levels were set at the flowering and fruit development stage (Stage I) and the fruit-ripening stage (Stage II), respectively. The Hydrus-1D model and field data were used to analyze the effects of deficit irrigation on tomato root growth, soil water uptake and utilization in the root zone. The results showed that deficit irrigation could reduce the total root length density of water-absorbed roots but increase the water-absorbed root length density of the underlying soil (30–60 cm). Moderate and severe water deficits at Stage II increased the water-absorbed root length density of the underlying soil by 0.10–6.26% and 2.12–11.71% compared with a mild water deficit. Considering tomato root growth, the Hydrus-1D model can improve the accuracy of soil moisture simulation. The main water absorption zone of tomato roots was 0–30 cm. Compared with full irrigation, the ratio of water absorption by the underlying root system (30–60 cm) to the total water absorption of the profile (0–60 cm) increased by 2.16–2.82% and 5.34–6.34% due to mild and moderate water deficits at Stage I. At Stage I and Stage II, a water deficit could reduce soil evaporation. T3 had the highest water use efficiency in two years, which was 24.07% (T9) and 20.47% (T8) higher than the lowest value, respectively. The optimal deficit irrigation scheme under this experiment condition is as follows: the soil water content was 70–90% θf (field capacity) at Stage I and was 40–60% θf at Stage II (T3).