Two new copper(Ⅱ) complexes [Cu(amp)Lx](ClO₄)₂(x=1, 2) were synthesized by self-assemble of 4-amino-2, 6-dimethoxypyrimidine(amp), organic polyamine N-(2-aminoethyl)-1, 3-propylamine) (L1), (bi(3-aminopropyl)-amine (L2) and copper salt using the solvent method. The products were characterized by means of elemental analysis, infrared spectroscopy, ultraviolet spectroscopy, powder X-ray diffraction, and scanning electron microscopy. The crystal structure of [Cu(amp)L2](ClO₄)₂ was analyzed by single crystal X-ray diffraction. The results indicates that [Cu(amp)L2](ClO₄)₂ belongs to monoclinic system, space group P2₁/c with a=1.207 90(12) nm, b=1.327 91(13) nm, c=1.390 39(14) nm, a=90°, b=90.056(3)°, γ=90°. In addition, the fluorescence spectrum shows that the ligand amp has an emission wavelength of 387 nm with a strong fluorescence value. However, when the amp coordinates with orgnic polyamines and copper to form a complex, significant fluorescence quenching occurs. This phenomenon indicates that amp interacting with the organic polyamines(L1, L2) have potential functions as fluorescent probes for copper ions. The antibacterial activity of the products in vitro were studied by agar plate diffusion method. The results show that the products have good antibacterial activity against the tested microorganisms.