The dataset addressed in this article relates to the research article entitled"Nicotabaflavonoidglycoside, the first example of cembranoid and flavonoid heterodimer from Nicotiana tabacum" (Yang et al., 2018) [1]. The dataset presents the MS4(879-571-421-335), MS n fragment pathways, (+) HR-ESI-MS, (-) HR-ESI-MS, UV, IR, 1H NMR, 13C NMR, HSQC, 1H-1H COSY, HMBC, ROESY, ORD and ECD data of Nicotabaflavonoidglycoside. The MS4(879-571-421-335), (+) HR-ESI-MS, (-) HR-ESI-MS, UV, IR, 1H NMR, 13C NMR, HSQC, 1H-1H COSY, HMBC, ROESY, ORD and ECD data were collected by experimental methods, and the MSn fragment pathways were acquired by analyses.