The chalcones (1,3-diaryl-2-propenones) and their derivatives are important intermediates in organic synthesis and have widespread applications in medicinal industry. The title choloro chalcone derivative, 3-(3-chloro-4,5-dimethoxyphenyl)-1-(4,5-dimethoxy-2-methyl phenyl) prop-2-en-1-one, has been synthesized. It is characterized by FTIR, 1 H NMR, 13 C NMR and single crystal X-ray diffraction. Title compound crystallizes in monoclinic space group C2/c with a = 23.540(11) Å, b = 9.738(4) Å, c = 17.305(7) Å, β = 106.37 (3)˚, V = 3806(3) Å 3 and Z = 8. The mean plane of the two substituted benzene rings is twisted by 66.29 (12)˚ with respect to each other. Ab-initio and density functional Theory (DFT) calculations have been carried out for the title molecule using RHF/6-311G and B3LYP/6-311G basis set respectively. The calculated results show that the predicted geometry can well reproduce structural parameters. In addition, frontier molecular orbitals and Mullikan charge distributions are carried out by using RHF and B3LYP methods. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Numbers of weak but significant interactions like C-H···O, C-H···π and π-π are involved in the stability of the structure. The weak π-π stacked interaction involves the centroids of the methyl phenyl rings with Cg-Cg separation distance of 3.857(2) Å. Synthesized compound has been screened for its antimicrobial activity against different panels of organisms.