A cis-configuration bis(4,5-diazafluorene-9-one thiosemicarbazone) palladium trihydrate, which exhibits approximately five times SHG (second harmonic generation) efficiency of urea, has been designed, synthesized, and structurally characterized. The complex, C24H16N10PdS2. 3H(2)O, crystallizes in trigonal space group P3(1) with cell parameters a = 10.749(2) Angstrom, c = 19.872(4) Angstrom, V = 1988.3(6) Angstrom(3), and Z = 3. The coordination geometry about the Pd(II) is surprisingly a cis-configuration square-planar formed by two imino nitrogen atoms N(3) and N(8) and two sulfur atoms S(1) and S(2) from two thiosemicarbazone ligands. Intramolecular contact analyses in the crystals and 1D and 2D H-1 NMR spectra in solution show that the cis-positioning of the two ligands was stabilized by the pi-pi interaction between the two delocalized diazafluorene moieties. Detailed crystal structure analyses demonstrate that both the intermolecular pi-pi stacking between the diazafluorene planes in different molecules and intermolecular hydrogen bonds between the water molecules and the deprotonated ligands might be the factors that influence the molecules to be packed in the acentric space group P3(1). The crystal structure of the free ligand was also reported here for comparison. The ligand, C12H9N5S, crystallizes in orthorhombic space group Pbca with cell parameters a = 8.432(2) Angstrom, b = 15.427(3) Angstrom, 17.387(3) Angstrom, V = 2272.7(8) Angstrom(3), and Z = 8. The thiosemaicarbazone moiety adopts an E configuration with N(1) cis to N(3).