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Fossil eggs of clam shrimps (Spinicaudata) are rare and little attention has been paid to the study of their shape and microstructures. Here, we report the discovery of exceptionally preserved three-dimensional eggs from numerous specimens of Eosestheria elliptica Chen, 1976 from the lacustrine Early Cretaceous Yixian Formation in western Liaoning, China. These three-dimensionally preserved fossil eggs display a spherical shape with smooth surface, part of the tertiary envelope, and possibly the first embryonic cuticle, which were previously unknown or ambiguous. The eggs are abundant and assumed to be attached to the exopod as in extant Spinicaudata. Moreover, the exceptional three-dimensional preservation and delicate preparation of slices of the eggs allowed us to document the microstructures and elemental composition of fossil eggs of clam shrimps from the Jehol Biota. Energy dispersive spectroscopy of the fossilized envelope revealed a calcium phosphate composition. However, the egg contents display two completely different elemental compositions. Some exhibit the same elemental composition as the envelope, whereas others has been replaced by alumino-silicate. The taphonomic process is also briefly discussed in this paper.