The characterization of nanoparticles morphology can be performed using TEM and high-resolution SEM. The primary difference between the two techniques is the way in which the nanoparticle images are resolved. SEM produces 3D images of particles while TEM produces 2D images. A high- resolution SEM secures resolution down to 1.2 nm while TEM resolves images down to 0.17 nm. SEM is well suited to looking at samples’ surface characteristics and TEM reveals composition details, such as a particle’s crystallinity and lattice structure.
See reference: https://www.azonano.com/article.aspx?ArticleID=4118
As Florian wrote, TEM is capable to resolve the crystal (atomic) structure of your sample. So you get information beyond shape and size. TEM reveals whether the particles are mono- or polycrystalline, and elemental analysis with EDS or EELS is possible with quite high resolution. If you have an appropriate instrument, you can also perform TEM-tomography to get 3D-information about your particle.