Sodium metal batteries (SMBs) are receiving broad attention due to the high specific capacity of sodium metal anodes and the material abundance on earth. However, the growth of dendrites results in poor battery performance and severe safety problems, inhibiting the commercial application of SMBs. To stabilize sodium metal anodes, various methods have been developed to optimize the solid electrolyte interphase (SEI) layer and adjust the electroplating/stripping behavior of sodium. Among the methods, developing anode host materials and adding electrolyte additives to build a protective layer are promising and convenient. However, the understanding of the interaction process between sodium metal and those organic materials is still limited, but is essential for the rational design of advanced anode hosts and electrolyte additives. In this study, we use copper(II) hexadecafluorophthalocyanine (F16CuPc), and copper(II) phthalocyanine (CuPc), as model systems to unravel the sodium interaction with polar functional groups by in-situ photoelectron spectroscopy and density functional theory (DFT) calculations. It is found that sodium atoms prefer to interact with the inner pyrrolic nitrogen sites of CuPc, while they prefer to interact with the outer aza bridge nitrogen atoms, owing to Na-F interaction at the Na/F16CuPc interface. Besides, for the both organic molecules, the central Cu(II) ions are reduced to Cu(I) ions by charge transfer from deposited sodium. The fluorine-containing groups are proven to promote the interaction process of sodium in organic materials, which sheds light on the design of functional interfaces in host materials and anode protective layers for sodium metal anodes.