ObjectivesTo compare the clinicopathological, molecular, and immune features of conventional and high‐grade transformation (HGT) secretory carcinoma (SC) in salivary glands.Materials and MethodsThe clinicopathological data of 88 cases including 74 conventional SCs and 14 SCs with HGT were reviewed. Targeted next‐generation sequencing was performed in 11 SCs with HGT and 7 conventional SCs. The level of PD‐L1 and CD8+ TILs was determined by immunohistochemistry.ResultsCompared with the conventional group, the rates of nodal metastasis, local recurrence, distant metastasis and mortality were significantly higher in the HGT cohort. Mutations of ARID1A/B, KMT2A, HOXD13, NRG1 and ETV6 genes were identified in HGT SCs. A recurrent E307G mutation in GATA6 gene was also observed in two cases. Two deceased HGT patients with distant metastasis harboured NOTCH3 mutations. ETV6‐RET translocation was prone to occur in the HGT SCs. Additionally, PD‐L1 expression was low, and CD8+ TILs were sparse in most HGT cases.ConclusionOur findings reveal novel gene alterations involved in the progression of HGT in SCs. Most HGT SCs patients cannot benefit from PD‐L1 blocking and may be approached with a distinct treatment strategy including the lymph node dissection and application of molecular target drugs in precision oncology.