Prunus (P.) humilis is a small woody shrub that has been widely planted in northern China due to its high nutritional value and resistance to environmental abiotic stress. However, little information about the responses of photosynthetic performance and the anatomical structure of P. humilis to saline–alkaline stress (SAS) under field conditions is available. Here, we investigated the behavior of the photosynthetic apparatus of P. humilis by measuring the chlorophyll fluorescence parameters under moderate (MS) and severe (SS) saline–alkaline stress and analyzing their relationship to leaf anatomical traits. The results showed that SAS significantly decreased the net photosynthetic rate (An) but increased the substomatal CO2 concentration (Ci). The maximum photochemical quantum yield of PSII (Fv/Fm) and the efficient quantum yield of PSII [Y(II)] decreased under MS and SS conditions, and this decrease was greater in the distal (tip) than in the proximal (base) leaf. Compared to the leaf tip, the base of P. humilis leaves seemed to have a stronger ability to cope with MS, as was made evident by the increased quantum yield of regulated energy dissipation in PSII [Y(NPQ)] and decreased excitation pressure (1-qP). Under MS and SS conditions, the shapes of the chlorophyll a fluorescence transient (OJIP) changed markedly, accompanied by decreased PSII acceptor-side and donor-side activities. The palisade–spongy tissue ratio (PT/ST) increased significantly with increasing stress and showed a significant correlation with the chlorophyll fluorescence parameters in the leaf base. These results suggested that the activity of PSII electron transfer in the upper leaf position tended to be more sensitive to saline–alkaline stress, and a chlorophyll fluorescence analysis proved to be a good technique to monitor impacts of saline–alkaline stress on photosynthetic function, which may reflect the non-uniformity of leaf anatomy. In addition, among the anatomical structure parameters, the palisade–spongy tissue ratio (PT/ST) can be used as a sensitive indicator to reflect the non-uniform of photosynthetic function and leaf anatomy under stress.