Abundant plant fossils were found in the Upper Miocene Shengxian Formation, eastern Zhejiang Province, China, among which Trapa belongs to a dominant population. The fossil fruits of Trapa were well preserved with abundant details. However, due to compaction during fossilization, Trapa fruits were often ?attened, leading to the loss of some characteristic features. Thereby, a bias in taxonomic and phylogenetic studies would occur when such studies were based on these fruit fossils. In this study, we present the first quantitative three-dimensional reconstruction of compressed Trapa fruit fossils to restore their original morphology prior to burial. This approach provides a novel perspective for the identification and classification of compressed fruit fossils. The three-dimensional reconstruction of Trapa fruit fossils enabled accurate comparisons with extant species. We subsequently identified it as a new species, named Trapa radiatiformis L. Xiao sp. nov., revealing differences from previously known taxa of Trapa. Importantly, our comparison suggests that the long lower horns and residual stalk may represent inherent characteristics of early Trapa fruits. However, these traits gradually degenerated during fruit evolution, resulting in morphological simplification during geological time. T. radiatiformis with primitive features exhibits good resemblance to Trapa natans fruit characteristics, which means it may be an ancestor of T. natans. We summarize the palaeogeographic distribution of fossil Trapa using previously published literature and demonstrate that the genus was most prosperous in the Miocene and exhibited the same distribution as that at present. Additionally, through detailed morphological comparisons between Trapa and Hemitrapa fruits, along with phylogenetic analysis within the Primotrapa genus itself, we propose a homology between Trapa and Hemitrapa, suggesting that they could have a common ancestor.