Reaction of a ditopic urea "strut" (L1) with cis-(tmen)Pd(NO3)2 yielded a [3+3] self-assembled molecular triangle (T) [L1 = 1,4-di(4-pyridylureido)benzene; tmen = N,N,N',N'-tetramethylethane-1,2-diamine]. Replacing cis-(tmen)Pd(NO3)2 in the above reaction with an equimolar mixture of Pd(NO3)2 and a clip-type donor (L2) yielded a template-free multicomponent 3D trigonal prism (P) decorated with multiple urea moieties [L2 = 3,3'-(1H-1,2,4-triazole-3,5-diyl)dipyridine]. This prism (P) was characterized by NMR spectroscopy, and the structure was confirmed by X-ray crystallography. The P was employed as an effective hydrogen-bond-donor catalyst for Michael reactions of a series of water-insoluble nitro-olefins in an aqueous medium. The P showed better catalytic activity compared to the urea-based ligand L1 and the triangle T. Moreover, the confined nanospace of P in addition to large product outlet windows makes this 3D architecture a perfect molecular vessel to catalyze Diels-Alder reactions of 9-hydroxymethylanthracene with N-substituted maleimide in the aqueous medium. The present results demonstrate new observations on catalytic aqueous Diels-Alder and Michael reactions in heterogeneous fashion employing a discrete 3D architecture of Pd(II). The prism was recycled by simple filtration and reused several times without significant loss of activity.