Three nickel substituted Keggin-type polyoxometalates, α-[SiW9O37{Ni(H2O)}3]−10 (denoted as SiW9Ni3), was intercalated into Zn3Al based Layered Double Hydroxide (Zn3Al-LDH) by the selective ion-exchange technique. The as-synthesized nanocomposite, SiW9Ni3@Zn3Al, was used as heterogeneous nanoreactor to promote the synthesis of drug-like aminoimidazopyridine small molecule skeletons via the well-known Ugi-type Groebke–Blackburn–Bienaymé reaction (GBB 3-CRs) in the absence of any acid/additive and under mild and solvent-free conditions. A synergistic catalytic effect between SiW9Ni3 polyoxometalate and Zn3Al-LDH precursors is evidenced by a higher catalytic property of the SiW9Ni3@Zn3Al composite compared to the individual constituents separately. Lewis/Bronsted acidity of the SiW9Ni3 polyoxometalate and Zn3Al-LDH precursors appear to be essential for the catalytic performance of the composite. Furthermore, the catalytic performance of SiW9Ni3@Zn3Al was also tested in GBB 3-CRs synthesis of amino imidazothiazole under mild and solvent-free conditions.