A series of zinc-based Metal-Organic Frameworks (MOFs) have been synthesized through the reaction of Zn(II) salts with amino acid derivatives Val-X [Val = N-(4-pyridylmethyl)-l-Valine, X = Cl−, HCOO−, CH3COO−] and Ala-X [Ala = N-(4-pyridylmethyl)-l-Alanine, X = Cl−, HCOO−]. The as-synthesized pristine Zn-MOFs adopt unique hexagonal coordination structures with robust amino and carboxylate sites. These pristine Zn-MOFs served as heterogeneous catalysts in Knoevenagel condensation reactions of aldehydes containing a variety of electron-donating and withdrawing groups with malononitrile or ethyl 2-cyanoacetate. These catalysts can promote these reactions in eco-friendly water/alcohol solvent media under mild conditions. High yields were achieved for both malononitrile and cyanoacetate products with E-isomer dominating for the latter. Furthermore, these catalysts can be recycled and reused for several times without losing catalytic activity significantly.