Abstract: Abstract: Carbon isotope discrimination value (Δ13C) was an integrative reflection to the rate of intercellular CO2 concentration(Ci) and air CO2 concentration (Ca) in a period, and Ci/Ca suggested a relative amount of photosynthetic rate (Pn) and stomatal conductance (gs) corresponding to CO2 demand and supply respectively, and then Ci/Ca would change significantly and affect the water use efficiency (WUE) ultimately with the variation of Pn or gs, which had the same impact factor with stable carbon isotope composition in crops. Δ13C and carbon isotope ratio (δ13C) could characterize the WUE during the entire life period of crops. Furthermore, the measurement for δ13C of different parts in crops could reflect cumulative WUE at different time scales, thus overcoming the limit of any other methods that could just measure instantaneous WUE at a time scale only. Therefore, Δ13C could well reflect water use efficiency at yield level (WUEET), and be used to infer instantaneous water use efficiency (WUEi) and intrinsic water use efficiency(WUEn) at leaf level, which was recognized as a reliable way to estimate the crop WUE at a long term. The current research on indicating the relationship between Δ13C of crop tissue and crop WUE were mainly focused on crops such as wheat, rice, sugar beet and maize under a water deficit, and less on tomatos under alternate partial root-zone furrow irrigation (AFI) and conventional furrow irrigation (CFI). In order to further investigate the water use mechanism on different parts of crops under different furrow irrigation, this research combined theoretical analysis with field experiments, integrating WUE research on different scales through carbon isotope's instruction on WUE, then analyzed the relationship between different parts of Δ13C in tomato with WUE at different scales to further explain the water use process and transferring rule in crop's different parts under partial root-zone irrigation. The experiment was carried out at the Experimental Station of Crop Efficient Water Use, Ministry of Agriculture in Wuwei city, Gansu province from May to September in 2011 and 2012 respectively. Leaf carbon isotope discrimination (ΔL), fruit carbon isotope discrimination (ΔF) values, and soil moisture, Pn, transpiration rate (Tr), gs, yield were measured and WUEi, WUEn, WUEET values were calculated. The results indicated that: ΔL, ΔF value was between 19.27‰ and 20.25‰, 18.07‰ and 20.04‰ respectively under different furrow irrigation in the fruit maturation period in 2011 and 2012. The ΔL value was significantly greater than ΔF value, indicating leaf carbon isotope discrimination was more sensitive to the response on different irrigation methods and irrigation quotas than fruit carbon isotope discrimination. ΔL showed a negative relationship with WUEi and WUEn respectively. Furthermore, ΔL showed a better indicating capacity on WUEn than WUEi under different furrow irrigation in the fruit maturation period, ΔL was significantly negative related with WUEn (R = -0.977, P<0.01) under the alternate partial root-zone furrow irrigation. ΔF had a better negative correlation with yield than ΔL. ΔL and ΔF both showed a negative relationship with WUEET. ΔL showed more significant correlation with WUEET and WUEn under AFI than CFI, indicating that AFI could regulate the photosynthetic capacity and improve water use efficiency more effectively and better reflect ΔL indicating capacity on WUE at different levels. In conclusion, using different tomato tissue Δ13C values to indicate WUE at different levels has a certain feasibility under different furrow irrigation in the northwest inland arid region, and also the leaf and fruit Δ13C values measured during the period of maturity can be a quantitative indicator to characterize accumulative WUE at leaf and yield levels of field tomato under furrow irrigation.