Three binuclear Cu(II) complexes of two pyrimidine derived Schiff base ligands, 2-S-methyl-6-methyl-4-formyl pyrimidine-N(4)-ethyl thiosemicarbazone (HL 1 ) and salicyl hydrazone of 2-hydrazino-4,6-dimethylpyrimidine (HL 2 ), have been prepared. HL 1 produces a bis(μ-thiolato) Cu(II) complex co-crystallizing with its mononuclear analog, [Cu 2 (L 1 ) 2 (NO 3 ) 2 ][Cu(L 1 )(NO 3 )] (1). On the other hand HL 2 shows versatility by producing two different classes of binuclear Cu(II) complexes, a bis(μ-phenoxo) complex [Cu 2 (L 2 ) 2 (NO 3 ) 2 ] (2) and another a (μ-4,4′-bipyridyl) complex, [Cu 2 (L 2 ) 2 (μ-4,4′-bipyridyl)(NO 3 ) 2 ] (3) under suitable conditions. All the three complexes show distorted square pyramidal geometry around each Cu atom but to a varied extent. Magnetic behavior of complex 1 shows that it is strongly ferromagnetic in nature whereas compounds 2 and 3 are weakly antiferromagnetic in nature. A magnetostructural correlation study combined with molecular modelling on complexes 1 and 2 has thrown light on the difference on magnetic interaction between the Cu atoms in these two complexes. Various factors that may be responsible for such differences are also explored. A novel and potentially useful pH dependant conversion of 3 to 2 has also been noticed.