In the present study, we focused on the optimal conditions for observation of morphology and atomic structure of carbon nanotube (CNT) in vivo by transmission electron microscopy (TEM). Either low-voltage or high-voltage TEMs was chosen for the high-contrast or high-resolution imaging of subcutaneous tissue and the multi-wall CNT (MWCNT). The morphology and structure of each cell organelle were well recognized using the low-voltage TEM at 75 kV. Individual MWCNTs forming the cluster were also visible by the low-voltage TEM. On the contrary, the high-voltage TEM image at 1250 kV shows poor contrast on both the cell organelles and MWCNTs. However, graphene layers of MWCNT were clearly visible in the HRTEM image using the high-voltage TEM. The influence of the surrounding biological tissue can be disregarded by the high-energy electrons due to their weak scattering/absorption effect in the tissue. It was indicated that the usage of the high-voltage TEM is quite effective to the atomic structure analysis of nano-crystalline materials in vivo.