The black rice anthocyanins are vulnerable to degradation due to the external environment, resulting in the destruction of local molecular structure, which reduces the nutritional value and health function. The stability of anthocyanin structure was improved by modifying anthocyanins with acyl groups provided by organic acids. The structural changes of anthocyanins modified by caffeic acid acylation were analyzed with Fourier transform infrared spectroscopy (FTIR). The results showed that the absorption peaks of functional group in 3 650~3 200 and 1 680~1 620 cm-1 were the same between both before and after anthocyanins modified, the phenolic hydroxyl absorption peak appeared in the fingerprint area of 1 282.68, 1 277.51 cm-1, and the alcoholic hydroxyl absorption peak appeared at 1 056.07, 1 054.03 cm-1, the absorption peak of C—H surface bending vibration in benzene ring appeared at 719.90 and 719.71 cm-1. It can be seen that the major structural framework of acylated black rice anthocyanins is still the aromatic ring structure of anthocyanins. In addition, the characteristic absorption peaks of conjugated carbonyl all appeared at 1 714.28 and 1 728.13 cm-1 in the area of 1 900～1 450 cm-1 both before and after the modification of anthocyanins, which corresponded to α-carbonyl structure in benzene ring, thus indicating the presence of acyl groups in the structure of the black rice anthocyanins. The new absorption peaks of modified anthocyanin appeared at 1 517.20 cm-1 in the infrared spectrum, which is right located in the stretching vibration zone of 1 800~900 cm-1 double bond (no hydrogen), the absorption peak of C—H surface bending vibration in benzene ring appeared at 876.65 cm-1 in the fingerprint region. At the same time, new fluctuations were observed at 2 500～2 000 cm-1 in the infrared spectrum after the second derivative treatment, which is the cumulative double bond stretching vibration region. The absorption peak of functional group at 3 370.20 cm-1 between 3 650~3 200 cm-1 is located in the multimolecular association region. It can be seen that when caffeic acid is used as acyl donor, the acylated modified black rice anthocyanins present a double acylated spatial structure due to the re-association of the molecules with the introduction of new acyl groups in the structure. The organic acid was linked to the sugar chain in the structure of black rice anthocyanin, and it was placed on the surface of 2-phenyl benzo pyran skeleton. This stacking model can resist water nucleophilic attack and other degradation reactions, which can improve the stability of black rice anthocyanin structure.