The experimental charge density in the chlorokojic acid crystal structure was investigated on the basis of high-resolution X-ray diffraction data collected at 80(2) K. The nature of chemical bonding and halogen interactions has been studied by means of deformation densities and by topological analysis using the Bader’s quantum theory of atoms in molecules (QTAIM). A comparison between the experimental and theoretical results, from calculations concerning gas phase and periodic DFT/B3LYP, was performed. For the intermolecular hydrogen bonds of O–H···O, C–H···O, and C–H···Cl types, full characteristics of bond critical points (BCP’s) were provided indicating closed-shell interactions. The topological analysis of charge density distribution revealed the presence of intermolecular C–Cl···O halogen bridge and halogen–halogen interactions of C–Cl···Cl–C type forming supramolecular Cl3 synthons, crucial for three-dimensional structure formation of chlorokojic acid. The pronounced anisotropy of electrostatic potential at the Cl atom clarifies both electrophilic and nucleophilic properties of the substituent.