A multilayer film that could selectively adsorb negatively charged molecules through layer-by-layer assembly of modified hyperbranched poly(ethylene imine) (BPEI) and poly(vinyl pyridine) (PVPy) via halogen bonding has been fabricated. To build up the film via halogen bonding, the BPEI modified with a donor of halogen bonding (BPEI-I) was firstly prepared by introducing the iodo-tetrafluorophenoxy group into the BPEI through a series of reactions. The BPEI-I was purified by dialysis and precipitation and the structure was determined by ¹H NMR. The BPEI-I could be layer-by-layer assembled with PVPy in the mixture solvents of tetrahydrofuran and chloroform. The UV-Vis spectrum was used to monitor the assembly process, which indicated that the assembly process was uniform. AFM was employed to observe the morphology and estimate the thickness of the resulting films, both of which confirmed the successful fabrication of the BPEI-I and PVPy multilayer. The driving force of the assembly was verified by XPS. The variation of the bonding energy of the N 1s and I 3d in the multilayer proved the halogen bonding between BPEI-I and PVPy. To demonstrate the selective adsorption, sodium anthracene-2-carboxylate (SAC) and 1-(anthracen-2-ylmethyl)pyridin-1-ium bromide (APB) was utilized as the probes, which resembled in the structure whereas had opposite charges. The adsorption was studied by UV-Vis spectra, which exhibited that the negatively charged SAC could be adsorbed by the BPEI-I/PVPy films, but the positively charged APB could not. In order to improve the stability of the film, as-prepared BPEI-I/PVPy films were further crosslinked by 1,3-dibromopropane. The resulting film still could selectively adsorb the small molecule with negative charge and moreover possessed higher stability. The ability of the BPEI-I/PVPy film to selectively adsorb negatively charged molecules could be attributed to halogen bonding, which provided the neutral environments, and the BPEI units, which offered the positive charged cavity to contain the objects. Such multilayer films could be potentially useful in the fields of biosensor, separation and micro-contact printing.