Drought is an important environmental factor that influences physiological processes in plants; however, few studies have examined the physiological mechanisms underlying plants' responses to continuous drought. In this study, the seedlings and younger individuals of Haloxylon ammodendron were experimentally planted in the southern part of the Gurbantunggut Desert. We measured their photosynthetic traits, functional traits and non-structural carbohydrate contents (NSCs) in order to assess the effects of continuous drought (at 15-day and 30-day drought points) on the plants' physiological responses. The results showed that at the 15-day (15 d) drought point, the leaf light-saturated net photosynthetic rate (An) values of both the seedlings and the younger individuals were decreased (by -68.9% and -45.2%, respectively). The intrinsic water use efficiency (iWUE) of the seedlings was significantly lower than that of the control group (-52.2%), but there was no diffenrence of iWUE observed in younger individuals. At the 30-day (30 d) drought point, a decrease in the An (-129.8%) of the seedlings was induced via biochemical inhibition, with a lower potential maximum photochemical rate (Fv/Fm, 0.42) compared with the control group, while a decrease in the An (-52.3%) of the younger individuals was induced due to lower stomatal conductance (gs, -50.5%). Our results indicated that prolonged drought induced a greater risk of seedling mortality as the relatively limited ability of stomatal regulation may increase the possibility of massive embolism, resulting in hydraulic failure.