Samara is the reproductive organ (seed) for many tree species in arid land in northwestern China. It is ecologically important in population development due to its dispersal function. However, information on its photosynthesis and effect of environmental stresses on its photosynthesis is still very limited. In the present study, responses of photosystem II (PSII) activity in samara and leaf of Siberian maple to short-term chilling/freezing and subsequent recovery potential were comparatively investigated by using polyphasic fluorescence test. The samara had more efficient photosynthesis (Fv/Fm and PIABS) and more efficient electron transport (φEo) but lower energy dissipation (DIo/RC) than leaf. Generally, the PSII performance and the electron transport for both samara and leaf were inhibited under low temperature stress, accompanied by an increase of energy dissipation in PSII reaction centers (RCs). PSII of both samara and leaf was not markedly affected by chilling and could acclimate to chilling stress. Short-term freezing could completely inhibit PSII activity in both samara and leaf, indicated by the drop of values of Fv/Fm, PIABS, φEo to zero. PSII functional parameters of short-term dark frozen samara could be largely recovered whereas those of frozen leaf could not be recovered. The higher tolerance of samara to short-term low temperature stress than leaf is of great ecological significance for seed development, population establishment of Siberian maple.