The responses of photosynthesis, chlorophyll fluorescence, and de-epoxidation state of the xanthophyll cycle pigments (DEPS) of micropropagated apple trees (Malus ×domestica) were investigated under whole-root water stress (WRS) and half-root water stress (HRS) induced by polyethylene glycol 6000 to simulate whole and partial root zone drying. Compared with control plants without water stress, plants under WRS and HRS exhibited reduced leaf net photosynthetic rate (Pn) and stomatal conductance (gS) with a greater reduction in WRS than in HRS plants. However, intercellular CO2 concentration (Ci) increased under WRS as water stress was prolonged, signifying a non-stomatal limitation of Pn. Regarding HRS, decreased Pn was mainly the result of a stomatal limitation explained by a relatively low Ci. Changes in photosynthesis and chlorophyll parameters indicate that severe and slight damage occurred to the photosynthetic apparatus of WRS and HRS leaves, respectively, starting at Day 3 after initiating water stress. This damage was not evident on the donor side but was expressed as a reduced capacity of the acceptor side of the photosystem II reaction centers. To prevent damage from excess light, the DEPS of WRS leaf increased. Decreased gS could explain reduced water use under an irrigation strategy of partial root zone drying in fruit trees.