Syntheses and characterizations of a Pd-based molecular triangle and square and hybrid composites with polyoxometalates are examined. The equilibrium between the Pd-based molecular triangle [(en*) Pd(4,4'-bpy)](3)( NO3)(6) and square [(en*) Pd(4,4'-bpy)](4)(NO3)(8) largely depends on the solvents, and both compounds have successfully been isolated: [(en*) Pd(4,4'-bpy)](3)(NO3)(6) center dot 3.5DMSO, monoclinic Cc(No. 9), a = 19.8210(2) angstrom, b = 34.3667(5) angstrom, c = 27.5484(4) angstrom, beta = 89.9420(10)degrees, V = 18765.5(4) angstrom(3); [(en*) Pd(4,4'-bpy)](4)(NO3)(8), monoclinic C2/c (No. 15), a) 45.6921(16) angstrom, b = 8.7721(8) angstrom, c = 36.719(3) angstrom, beta = 126.509(2)degrees, V = 11829.4(14) angstrom(3). The reactions of the Pd-based molecular triangle/square with [W6O19](2-), [W10O32](4-), and [alpha-SiW12O40](4-) form {[(en*) Pd(4,4'-bpy)](4)[ superset of W6O19]}[W6O19](3), {[(en*) Pd(4,4'-bpy)](4)[superset of W6O19]}(NO3)(6), {[(en*) Pd(4,4'-bpy)](4)[superset of W10O32]}[W10O32], [(en*) Pd(4,4'-bpy)](4)[W10O32](2), and [(en*) Pd(4,4'-bpy)](4)[alpha-SiW12O40](2). The molecular square does not encapsulate the largest [alpha-SiW12O40](4-), but it does encapsulate [W6O19](2-) and [W10O32](4-). The isolation of [W6O19](2-) and [alpha-SiW12O40](4-) from the mixture by use of the molecular square is possible by utilizing the quite different solubility of {[( en*) Pd( 4,4'-bpy)](4)[superset of W6O19]}(NO3)(6) and [(en*) Pd(4,4'-bpy)](4)[alpha-SiW12O40](2) formed in DMSO. The size-selective encapsulation property of supramolecules may open the new way to rationalize isolation methods of the useful polyoxometalates.