In this study, Lycium barbarum was use as experimental material, ultrathin section technique, microscopy and transmission electron microscopy were employed to analyze the changes of microstructure and ultrastructure of leaves and young roots of L. barbarum under different NaCl concentrations. The results showed that, with the increase of NaCl concentration, (1) the upper epidermal cells of the leaf became thicker, and the cells of fenestrations tissue appear shortened, became loose and disordered, the primary structure of the young roots did not change significantly. (2) The chloroplasts in fenestrated tissues of the leaves no longer adhered to the cell membrane, the double layer membrane of chloroplasts was damaged, the basal lamellae was arranged loosely, disorganized, swollen and vacuolated, the number of starch grains and osmiophilic granules increased, slight changes in mitochondria in chloroplasts. The shape of mitochondria in the cortical cells has changed, the structure was damaged, the inner and outer membranes were blurred or even ruptured, most cristae were blurred, vacuolation was occurred. The cell nucleus disintegrated and the content matrix flowed out. The study showed that different concentrations of NaCl stress had different effects on the microstructure and ultrastructure of the leaves and young roots of L. barbarum. The microstructure and ultrastructure of the leaves and young roots of L. barbarum were significantly changed at NaCl concentrations greater than 200 mmol/L. The changes of mitochondria in the leaf pulp cells were not as significant as those of chloroplasts, and it was assumed that the salt tolerance of mitochondria in the leaf pulp cells was stronger than that of chloroplasts.