Organic anode materials have attracted considerable interest owing to their high tunability by adopting various active functional groups. However, the interaction mechanisms between the alkali metals and the active functional groups in host materials have been rarely studied systematically. Here, a widely used organic semiconductor of perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) was selected as a model system to investigate how alkali metals interact with imide functional groups and induce changes in chemical and electronic structures of PTCDI. The interaction at the alkali/PTCDI interface was probed by in-situ X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), synchrotron-based near edge X-ray absorption fine structure (NEXAFS), and corroborated by density functional theory (DFT) calculations. Our results indicate that the alkali metal replaces the hydrogen atoms in the imide group and interact with the imide nitrogen of PTCDI. Electron transfer induced gap states and downward band-bending like effects are identified on the alkali-deposited PTCDI surface. It was found that Na shows a stronger electron transfer effect than Li. Such a model study of alkali insertion/intercalation in PTCDI gives insights for the exploration of the potential host materials for alkali storage applications.