Two Keggin-type polyoxogermanotungstates [M(phen)₃]₂[GeW₁₂O₄₀]·2H₂O (M=Zn (1), Co(2)) were synthesized by hydrothermal method. Compounds 1 and 2 are isomorphic, with the Pnma space group. 2D layers are linked by the hydrogen bonds between ligands and cluster anions. The layers were connected to form a three-dimensional supramolecule by strong molecular inter-atomic forces between adjacent phenanthroline. The compounds were characterized by XRD, FTIR, two-dimensional (2D) correlation infrared spectroscopy under magnetic and thermal perturbation, TG, etc. XRD showed that the spectrum was consistent with the simulation by single crystal structure data, and the main peaks were the same, indicating that the synthesized compound was relatively pure. The FTIR spectrum indicated that the wide absorption peak was ν_as(O—H)near 3 400 cm^-1, the peak between 1 650 and 1 350 cm^-1 was the skeleton stretching vibration peak of the aromatic ring, and there was four characteristic stretching vibrations of Keggin cluster anion skeleton in the range of 1 100 to 700 cm^-1. Furthermore, the two-dimensional infrared correlation spectroscopy under 5~50 mT magnetic showed that the obvious difference between compound 1 and compound 2 in the range of 1 300~1 500 and 3 000~3 300 cm^-1 may be caused by the transition metal (Zn(Ⅱ), Co(Ⅱ)) in the compounds which assigned to the C—C skeleton of phen and C—H…π hydrogen bond varies. TGA showed that the weight loss process could be divided into three stages. In the first stage, the free water was lost, and in the second, the coordinated phen was lost. At last, in the third stage, the framework of the tungsten oxide cluster began to collapse from 620 ℃. Results of the experiment on antitumor activities in vitro showed that two compounds inhibited five different human cancer cell lines (gastric cancer cell line, HGC-27 and SNU668; liver cancer cell line Huh7; and colon cancer cell line HCT116 and SW480) demonstrated dose dependency and selectivity. It was found that the IC₅₀ of the two compounds against the five kinds of human tumor cells was less than 100 μmol·L^-1. The synergistic effect of the organic ligand and cluster anions enhanced the antitumor activity of compounds 1 and 2 compared to unmodified POM. The two compounds showed the highest antitumor activity against colon cancer cell SW480 and the lowest inhibitory effect against gastric cancer cell SNU668. Although compounds 1 and 2 isomorphisms, the transition metal is different, lead to varying widely in their antitumor activity, compound 2 the inhibitory effect of five kinds of human tumor cells better than compound 1, the compound 2 for inhibition of colon cancer cells SW480 was 2.7 times than that of compound 1. The varied antitumor potencies of title compounds can provide direction for further research into the development of POM drugs.