Updated project metadata. Lonicera japonica Thunb is a typical Chinese medicinal material with the homology of medicine and food. Post-translational modification (PTM) of proteins can significantly affect protein structure and function, and plays a very important regulatory role in plant development. However, to date, little is known about the functions of PTM in L. japonica. Therefore, the study of lysine succinylation during the floral developmental stages will help to understand the mechanism of the secondary metabolism of L. japonica. In this study, we first analyzed lysine succinylation exist in L. japonica, and found lysine succinylation is highly abundant in juvenile bud stage than gold flowering stage. Then a highly efficient enrichment method for succinylation peptides was used to identify 586 succinylation modification sites in 303 proteins in L. japonica. Our bioinformatics analysis further revealed that the succinylated proteins are involved in many important biological processes including TCA, amino acid metabolism and secondary metabolism. With the development of flowering stage of L. japonica, the succinylation degree of aspartate transaminase was up-regulated while 4-coumarate-CoA ligase was down-regulated, suggesting that succinylation of proteins is important for the bioactive compounds’ biosynthesis process in L. japonica. Protein modification in vitro also verified the impact of succinylation on both 4CL and AT enzyme activity would be changed. As a consequence, current examine provides new insight into the molecular mechanism underlying the accumulation of active ingredients in L. japonica at the post-translational modification level.