Transmission electron microscopy (TEM) is indispensable to reveal the cellular nanostructure of the 2:17-type Sm-Co based magnets which act as the first choice for high-temperature magnet-associated devices. However, structural deficiencies could be introduced into the TEM specimen during the ion milling process, which would provide misleading information to understand the microstructure–property relationship of such magnets. In this work, we performed a comparative investigation of the microstructure and microchemistry between two TEM specimens prepared under different ion milling conditions in a model commercial magnet Sm13Gd12Co50Cu8.5Fe13Zr3.5(wt.%). It is found that additional low-energy ion milling will preferably damage the 1:5H cell boundaries, while having no influence on the 2:17R cell phase. The structure of cell boundary transforms from hexagonal into face-centered-cubic. In addition, the elemental distribution within the damaged cell boundaries becomes discontinuous, segregating into Sm/Gd-rich and Fe/Co/Cu-rich portions. Our study suggested that in order to reveal the true microstructure of the Sm-Co based magnets, the TEM specimen should be carefully prepared to avoid structural damage and artificial deficiencies.