Alternate partial root-zone irrigation (APRI) can improve water use efficiency in arid areas. However, the effectiveness and outcomes of different frequencies of APRI on water uptake capacity and physiological water use have not been reported. A two-year field experiment was conducted with two irrigation amounts (400 and 500 mm) and three irrigation methods (conventional irrigation, APRI with high and low frequencies). Root length density, stomatal conductance, photosynthetic rate, transpiration rate, leaf water use efficiency, midday stem and leaf water potentials were measured. The results show that in comparison with conventional irrigation, APRI with high frequency significantly increased root length density and decreased water potentials and stomatal conductance. No differences in the above indicators between the two APRI frequencies were detected. A significantly positive relationship between stomatal conductance and root length density was found under APRI. Overall, alternate partial root-zone irrigation with high frequency has a great potential to promote root growth, expand water uptake capacity and reduce unproductive water loss in the arid apple production area.