The complex with the molecular formula of Zn(Phen)(NAA)2 was synthesized by the reaction of ZnSO4, naphthylacetic acid and phenanthroline in ethanol-water solution at about pH≈7. It was characterized by elemental analysis, IR spectrum and X-ray single crystal diffraction. The antibacterial activity on E. Coli, S. Aureus and B. Subtilis were also been studied. The crystal of the complex belongs to triclinic system with space group P1, a=1.300 2 nm, b=1.306 4 nm, c=1.714 4 nm, α=89.41°, β=77.06°, γ=86.70°, V=2.833 5(2) nm3, Z=4, Dc =1.444 g·cm-3, Mr=615.96, μ(Mo Kα)=0.912 mm-1, the final R=0.039 8 and wR=0.103 4 [I>2σ(I)], F(000)=1 272. An asymmetry unit is composed of two independent molecules of Zn(Phen)(NAA)2 with different bond length and bond angles. There exist two kinds of face to face π-π stacking interactions . The complex has a good effect against E. Coli. CCDC: 619222.