The effect of low temperature on leaf anatomy and photosynthetic performance of two wheat (Triticum L.) genotypes grown after rice (Oryza sativa L.) was investigated. After exposure to low temperature, the arrangement of mesophyll cells in cv. Zhengmai 9023 (poor cold tolerance) was more irregular than cv. Yannong 19, being a cold tolerant variety. Mesophyll cells shrank, and its vessels and sieve tubes ruptured at the tillering stage. Net photosynthetic rate (Pn), intercellular CO2 concentration (Ci), and stomatal conductance (Gs) declined significantly in the low temperature treatment compared with control across both cultivars, but the decreased amplitude in Pn and Gs were greater for cv. Zhengmai 9023 than cv. Yannong 19. Compared with the control, initial fluorescence (Fo), non-photochemical quenching (NPQ), and the acyclic photosynthetic electron transfer rate of PSII (ETR) generally increased, but the maximum photochemical efficiency of PSII (Fv/Fm) and the photochemical quenching coefficient (qP) generally decreased in low temperature treatment. After the low temperature treatment, the increase in Fo parameter of cv. Zhengmai 9023 was greater than cv. Yannong 19. In contrast, the decreases in Fv/Fm, qP, and ETR were greater for cv. Zhengmai 9023 than cv. Yannong 19, but the increase in NPQ in Yannong 19 was greater than Zhengmai 9023. The results suggest that exposure to low temperatures at the tillering and stem elongation stages can significantly affect leaf anatomy and photosynthetic performance in wheat. Meanwhile, the photosynthetic apparatus was damaged only slightly and showed a high level of photosynthetic activity and a strong self-protection mechanism when the strong cold tolerance cultivars were chosen.