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Lonicerae japonicae Flos, a traditional Chinese medicine, has the function of evacuating heat and detoxifying. To promote the optimization of Lonicerae japonicae Flos germplasms and improve the quality of medicinal materials, 55 batches of five Lonicerae japonicae Flos germplasms with the same origin were collected during different periods, a UHPLC‐TOF‐MS method was established, and 22 kinds of phenolic acids were found and qualitatively analysed. Seventeen phenolic acids were selected for quantitative analysis by UHPLC‐QqQ‐MS/MS, and the quantitative results were analysed by principal component analysis, orthogonal partial least squares‐discriminant analysis, and partial least squares discriminant analysis. The contents of phenolic acids in periods S1–S6 were found to be significantly different. There were also significant differences in the accumulation of phenolic acids in Lonicerae japonicae Flos during different growth periods. Ferulic acid, 5‐O‐caffeoylquinic acid, and caffeic acid were determined to be important components to distinguish the different growth periods of Lonicerae japonicae Flos. There were significant differences in the phenolic acid content of different germplasms of Lonicerae japonicae Flos, and the total amount of 17 phenolic acids and total acids (chlorogenic acid, 3,5‐di‐O‐caffeoylquinic acid, and 4,5‐di‐O‐caffeoylquinic acid) in "Hua Jin No. 6" was highest, so the quality of "Hua Jin No. 6" was better than that of the four other germplasms. In addition, chlorogenic acid methyl ester and caffeic acid were the smallest markers in combination to distinguish the five germplasms of Lonicerae japonicae Flos. [ABSTRACT FROM AUTHOR]