Phloem girdling can cause decline of photosynthetic rate (Pn), and the reason for Pn decline had been attributed to the reduction of stomatal conductance (Gs) and end-product feedback inhibition. In order to explore the reason for Pn decline, the different stages of girdling—control, semi-girdling (SG), and full-girdling (FG)—were performed on Alhagi sparsifolia Shap. (Fabaceae) on the southern rim of the Taklamakan Desert. Our results showed that on the 1st day, abscisic acid (ABA) content and water use efficiency (WUE) increased, and Gs, Pn, and transpiration rate (Tr) decreased in the full-girdled leaf. On the 30th day, leaf ABA content, leaf starch content, and leaf soluble sugar content increased in the full-girdled leaf, and Gs, Pn, Tr, WUE, root starch content, root soluble sugar content, chlorophyll (Chl) content, maximum photochemical efficiency (Fv/Fm), and leaf water potential (Ψleaf) all decreased in the full-girdled leaf. SG showed no physiological change on the 1st day, whereas on the 30th day, the change was similar to FG, although the degree was less. The result of the present work implied that the reason for Pn decline in girdling may depend on time. In the short term, girdling (FG)-induced Pn decline was due to ABA accumulation, which resulted in the reduction of Gs. In the long term, however, Pn decline caused by girdling was due to many factors, including Gs reduction, which resulted from ABA accumulation, carbohydrate feedback inhibition, degradation of Chl content, decreasing of Fv/Fm, and deterioration of Ψleaf. In addition, a portion (half) of the phloem cannot undertake the transport work conducted by the whole phloem, and thus the girdled half circle of the phloem would lead to a similar effect to FG in the long term, although the degree was less.