Electron backscatter diffraction (EBSD) has been widely used in recent studies of eggshells for its convenience in collecting in situ crystallographic information. China has a wide variety of dinosaur eggshells, although nearly none have been studied with this technique. Elongatoolithid eggs include many oogenera, although the microstructural differences of some were not highly appreciated, leading to several parataxonomic problems. In this paper, we surveyed seven elongatoolithid oogenera in China using EBSD in order to acquire more information about their microstructural variation. It is shown in this paper that in some elongatoolithid eggshells, scaly calcite grains that form the squamatic ultrastructure are not the only form of calcite in the continuous layer. Large columnar grains separated by high-angled grain boundaries and slender subgrains separated by radially arranged low-angled grain boundaries could exist in certain areas of the eggshells such as Macroolithus and Macroelongatoolithus. This paper discusses the criteria for identifying squamatic ultrastructure and proposes type I (rich in rugged high-angled grain boundaries) and type II (rich in both rugged high- and low-angled grain boundaries) squamatic ultrastructures. A pathological layer is found in Undulatoolithus pengi. An external zone is identified in the eggshell of Heishanoolithus changii, which does not support its position within the oofamily Elongatoolithidae. We argue that Paraelongatoolithus no longer belongs to Elongatoolithidae based on a combination of reticulated ornamentation, columnar continuous layer, and acicular mammillae. The high structural variation in elongatoolithid eggshells also implies that it may be inappropriate to relate all previous elongatoolithid eggshells to oviraptorosaurs and assume they are non-monophyletic.