Dens invaginatus (DI) is a developmental anomaly of teeth. Here we observed the characteristics of DI in 517 permanent teeth from 67 ancient Chinese people using micro-computed tomography (micro-CT) scanning techniques. The individuals were excavated from Shaanxi province of China and identified to be about 2,000 years old. Four DI categories are proposed to distinguish the different types of DI. The invaginated lingual fossa is classified into three classes. The overall prevalence of DI in 67 individuals was 31.34% (21 of 67). DI was found in 25 of 517 teeth (4.83%). All affected teeth were maxillary lateral incisors. The invaginated lingual fossa (Type I DI) occurred most frequently (84%), followed by radicular grooves (Type II; 16%), while Type III and Type IV were not found in the present study. Some of fossae correspond with radicular grooves (8 of 21; 3 located at mesial, 5 were distal). The bilateral incidence of DI was 19.05%. Comparing our results to those of a retrospective survey of DI from 1873 to present, we found a higher rate of DI in the excavated teeth of Chinese individuals 2,000 years ago. The use of the micro-CT technique and ethnic origin might have contributed to the higher incidence of DI.