The Ediacaran to Cambrian transition is a critical interval of time during which major evolutionary changes occurred. Recently, abundant Protoconites minor have been recovered from the silty shales of the lower Cambrian Yanjiahe Formation (Terreneuvian, Fortunian - Stage 2) in the Three Gorges area of South China. These fossils represent an important ecological diversification of macroscopic organisms at the onset of the Cambrian. Protoconites minor is a probable cnidarian-grade organism preserved by carbon compression. Herein, geometric morphometric analyses are applied to crack out specimens of P. minor to reveal any cryptic morphological details that may have implications for their morphological diversity, ontogenetic processes, and taxonomic identification. These statistical analyses reveal a strong relationship between size and shape, which indicates that the overall shape of P. minor was mainly controlled by allometric growth. The smaller specimens are generally wider at the anterior and more commonly have straight-sides. Larger individuals tend to be narrower at the anterior, with bending more common. Our analyses demonstrate that there are transitional forms between larger, strongly bent specimens and smaller, straight specimens, suggesting that the assemblage likely consists of a single species.