Objective To investigate the differences between red-fruit and yellow-fruit ginseng from the perspective of compositional tissue distribution using mass spectrometry imaging technology.Methods Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) is employed to visually characterize saponin components in fresh ginseng tissues with two distinct fruit colors. Additionally, the total saponin, total flavonoid, and total polysaccharide content in the samples are quantitatively determined.Results Under the condition of mass spectral errors below 15 mg/kg, a total of 14 saponin components, including malonylated ginsenosides such as mRb1, are identified. Significant spatial distribution differences in saponins are observed across tissues within the same fruit color. Specifically, the cambium predominantly contains Ginsenoside Rh4, the cortex is dominated by mRb2/mRc, the phloem primarily contains mRb1, and the xylem is characterized by Ginsenoside Ro. Comparative analysis reveals that red-fruit ginseng exhibits higher content of mRb1, mRb2/mRc, and mRg1/mRf, whereas yellow-fruit ginseng shows greater abundance in mRe and Ginsenoside Ro. Furthermore, the total polysaccharide and flavonoid content are significantly elevated in red-fruit ginseng, while yellow-fruit ginseng demonstrates higher total saponin content.Conclusion This study systematically elucidates the distinct differences in the content of saponins and other chemical components between red-fruit and yellow-fruit ginseng.