Four new polynuclear clusters [NaMnIII3MnII(HL)3(μ4-O)(μ1,1-N3)3]ClO4·CH3CH2OH·(H2O)3 (1), [NaMnIII3MnII(HL)3(μ4-O)(μ1,1-N3)2(μ1,3-N3)]ClO4·CH3CH2OH·H2O (2), [NaMnIII3MnII(HL)3(μ4-O)(HCOO)3]ClO4·(H2O)4 (3) and [NaMnIII3MnII(HL)3(μ4-O)(PhCOO)(H2O)2](ClO4)2·H2O·PhCOO·PhCOOH·CH3OH (4) have been obtained via self-assembly between 3-((2-hydroxy-3-methoxybenzylidene)amino)propane-1,2-diol (H3L: condensed from o-vanillin and 3-amino-1,2-propanediol) and the auxiliary bridges (N3−, HCOO−, PhCOO−, H2O) with Mn(ClO4)2·6H2O in the air-exposed methanol solution. The structures of 1–4 all contain [NaMnIII3MnII] units and show a very similar trigonal propeller-like shape. The valences of the metal ions were determined by detection of the Jahn–Teller distortion visible for MnII,III, and confirmed by bond-valence sum (BVS) calculations. Three MnIII ions and one MnII ion take the shape of a super-tetrahedron with the MnII ion lying above the triangular [Mn3O] plane constructed from three MnIII ions linked by a central μ4-O atom. The NaI ion which lies below the [Mn3O] plane is linked with MnIII ions through the oxygen atoms from Schiff base ligands. The main structural difference in the four clusters is caused by the different bridging modes among MnIII ions. A structural comparison of 1–4 demonstrates that the auxiliary ligands play a key role in governing the coordination motifs. Moreover, the magnetic properties of these clusters exhibit dominating antiferromagnetic exchange interaction between spin carriers of MnII,III.