Experiments of alternate partial root-zone irrigation (APRI) on tomato plants were conducted in the field with three different water application rates via furrow irrigation (i.e., AFI) during 2011–12 and drip irrigation (i.e., ADI) during 2013–14 in the arid region of northwest China. Leaf carbon isotope discrimination (ΔL), fruit carbon isotope discrimination (ΔF) and fresh yield (Y) were determined at fruit maturation stage. The impacts of irrigation treatments on water use efficiency (WUE) were evaluated at leaf and yield scales. The results showed that APRI usually resulted in a higher WUE improvement with no significant difference in yield but 33.3% less irrigation water. Compared with conventional irrigation (CI), APRI regulated leaf photosynthetic processes and stomatal aperture more efficiently and induced a lower ΔL and higher WUE at leaf scale. Δ13C of tomato leaf and fruit at fruit maturation stage could be used as an important, quick and suitable indicator for phenotype of high WUE at both leaf and field scales to some extent, irrespective of which APRI method was applied. Our results suggest that APRI, especially ADI, have some potential to be used as an efficient water-saving irrigation strategy in arid region of northwest China where tomato production is threatened by insufficient irrigation water for agriculture.