Single-celled diatoms have attracted much attention due to their delicate nanostructures and wide applications in photonics, biology, nanofluidics, drug delivery, and so on. Three-dimensional (3D) surface reconstruction of diatoms has profound significance both in theory and in applications. The scanning electron microscope (SEM) stereo imaging technique was used to reconstruct the surface features of the diatomaceous frustules to quantitatively evaluate specimens. Geometrical parameters such as volume and area were given based on the reconstructed 3D image. This approach provides a simple and efficient way to measure the morphological parameters of diatoms at nanometer scale in three dimensions.