This study describes and illustrates a new species of Trachydium (Apiaceae). The new species was discovered in high-altitude stony deserts at an elevation of 4,800–5,200 m in Nyalam County, Xizang, China. It resembles Trachydium roylei Lindl (type species of Trachydium) in overall morphology, especially in fruit characteristics: scattered tubercles on the fruit surface, vittae in the commissural characteristics. However, significant differences were observed between the new species and T. roylei: 1–2-pinnate basal leaves (vs. 2–3-pinnate), ovate ultimate leaf segments (vs. linear-lanceolate), broadly membranous-margined pinnatifid bracteoles (vs. pinnate), 14–22 rays (vs. 5–10), triangular calyx teeth (vs. obsolete), and subpentagonal endosperm in transverse section (vs. suborbicular). In addition, we also studied the pollen micromorphology and found that it was also similar to T. roylei. Furthermore, to clarify the systematic position of the new species, the Internal Transcribed Spacer (ITS) region was sequenced to reconstruct the phylogeny by Maximum Likelihood analysis (ML) and Bayesian Inference (BI). The results showed that the topologies of phylogenies reconstructed by ML and BI analyses were identical and robustly supported the new species as sister to T. roylei (ML/BS = 88, BI/PP = 0.99). Moreover, the genetic distance (0.0328) confirmed its independent species status. Therefore, a combination of morphology, micro-morphology of pollen and phylogenetic analyses confirms the distinct species status of Trachydium nyalamense W.Y. Tan, Z.X. Li & X.J. He, sp. nov.