Three sandwich-type TM-containing (TM = transition metal) organophosphonate-based polyoxotungstate clusters, [TM(H2O)4(SeW6O21)2{Co(OOCCH2NCH2PO3)2}3]12- (TM = Co, Ni), have been successfully synthesized, which are the first reported TM-containing organophosphonate-based selenotungstates. They were structurally characterized by PXRD analyses, IR spectroscopy, TGA analyses, etc. Magnetic measurements show that all three compounds exhibit antiferromagnetic interactions. Besides, Co1 can be used as an efficient heterogeneous catalyst in the Knoevenagel condensation of benzaldehyde and ethyl cyanoacetate under mild conditions (60 °C), and exhibits satisfactory conversion (93%) and high selectivity (99%).