We demonstrated tomographic phase microscopy (TPM) of living diatoms in liquid in order to quantitatively analyze localization of cell components of symmetric shape cells. One TPM image includes several millions of pixel data of three-dimensional optical information such as refractive index (RI) values of cell components. In this work, the obtained TPM data of living cells were analyzed using X-Y cross sections to visualize the localization of cell components. Distribution of RI values at the cell surfaces and inside the cells were quantified. The results showed that the RI values were slightly lower at the cell center (RI ∼1.400) than the cell boundary (RI ∼1.420). RI values were fluctuated according to the depth measured from the cell surface also. Furthermore, statistical analysis by root mean square and Moran's I methods revealed unique localization of RI values for several cells among 25 individuals. In addition, the volumes of the cells estimated using TPM data corresponded to the cell volumes obtained via scanning electron microscopy. Our work proposed an effective procedure to quantitatively/statistically investigate intracellular materials of living cells based on physical information of TPM data.