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Objective To use the high-performance liquid chromatography (HPLC) method and desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) method to study the dynamic accumulation and distribution of secondary metabolites of Coptis chinensis in different growth years. Methods Using the samples of one-, three-, and five-year Coptis chinensis as the research object, the HPLC method was used to determine the contents of seven index components (jatrorrhizine hydrochloride, columbamine, epiberberine, coptisine hydrochloride, palmatine hydrochloride, berberine hydrochloride, and magnoflorine) as the secondary metabolites of Coptis chinensis. Further, the distribution of seven index components in the one-, three- and five-year Coptis chinensis slices were qualitatively analyzed by using the DESI-MSI method. Results The HPLC result showed that the contents of berberine hydrochloride and palmatine hydrochloride, jatrorrhizine hydrochloride, columbamine, and magnoflorine in five-year Coptis chinensis were the highest; coptisine hydrochloride and epiberberine reached the highest level in 3- year Coptis chinensis, while the contents of magnoflorine and jatrorrhizine hydrochloride were the lowest in three-year Coptis chinensis; and berberine hydrochloride, palmatine hydrochloride, columbamine, epiberberine, and coptisine hydrochloride were the lowest in one-year Coptis chinensis. The hydrochloride of each alkaloid was dissociated in the process of mass spectrometry and appeared in the prototype form. The result obtained by the DESI-MSI method show that berberine and epiberberine were concentrated in the whole-slices section, the distribution area of the one-year sample was the smallest, and the distribution areas of the three- and five-year samples were similar. Jatrorrhizine and columbamine were distributed in the phloem and pith, and the five-year sample distribution area was the largest; palmatine and coptisine were distributed in the phloem and pith, and the one-year sample distribution area was the smallest. Magnoflorine was only distributed in the wood, and the distribution areas in the one-, three-, and five-year Coptis chinensis were similar. Conclusion The accumulation of secondary metabolites in the one-year samples was the least, indicating that the first year is the main stage of the growth and development of Coptis chinensis. The accumulation of secondary metabolites of three-year samples was higher than those of the one-year sample, indicating that the following one to two years are the main stage for the accumulation of secondary metabolites of Coptis chinensis. The five-year plant sample had the highest content of total components, and berberine accumulated the most, which is consistent with the market usage rules of Coptis chinensis being cultivated for at least five years. [ABSTRACT FROM AUTHOR]