In this study, we used 5 Osmanthus fragrans varieties as materials, with Hoagland culture liquid as control, 2 NaCl contents (70 and 100 mmol/L) as treatments, and observed the ultrastructure characteristics of different varieties with by TEM and SEM after 10 d treatment, to clarify the anatomical structure response mechanism of O. fragrans cultivars to NaCl stress tolerance. The results showed that: (1) TEM analysis showed that the chloroplast structure in mesophyll cells of 5 varieties are destroyed in different degrees with the increase of NaCl concentration; the nucleus structure of 5 varieties maintain normal in 70 mmol/L NaCl; in 100 mmol/L NaCl, chromatin within the nucleus begins to degrade. With the NaCl stress strengthening, osmiophilic particles in the thylakoid lamellar structure of the 5 varieties increase significantly. In terms of membrane structures, the mesophyll cells of ‘Daye Yingui’are damaged most seriously, chloroplast membranes are damaged so that the basic shape cannot be recognized. (2) SEM photos indicated that the stomatal density on leaf surface of 5 varieties increases gradually while the opened porosity density decrease with the increase of salt concentration. The proportion of palisade tissue accounting for leaf thickness of ‘Daye Yingui’, ‘Xiao Qiufeng’ and ‘Wanzi Yingui’ increase at first then decrease with the increase of salt concentration of ‘Huangchuan Jingui’ and ‘Zigeng Ziyingui’. It proves that the higher the salt concentration was，the more obvious of the damage effect was. This experiment can preliminarily judge that the salt stress tolerance of ‘Daye Yingui’, ‘Xiao Qiufeng’ and ‘Wanzi Yingui’ is slightly higher than that of ‘Huangchuan Jingui’ and ‘Zigeng Ziyingui’.