The search for functional materials, for example those aiming at microelectronics, magnetic recording, and catalysis, often ventures into mixed metal systems to achieve optimization of the properties. Thus, understanding site preference and self-organization is crucial but hard to implement. Herein, we present a system whereby MgII, MnII, and MnIII ions selectively locate exact positions within the Brucite-structured cluster, Mn13Mg6, [MnIII⊂MgII6⊂MnII9MnIII3( L)18(OH)12(N3)6](ClO4)6·12CH3CN, H L = 1-(hydroxymethyl)-3,5-dimethylpyrazolate). The MnIII being small (78 pm) takes up the core position; while 6 MgII (86 pm) are located in the inner ring, and the 9 large MnII (97 pm) and 3 MnIII occupy the outer ring. The factors (a) ionic radii, (b) regularity in coordination geometry, oxophilicity, and softness of MgII compared to MnII, and (c) Jahn-Teller distortion of MnIII may all be implicated synergistically. Electrospray ionization mass spectrometry reveals the M19 disc remains an integral unit when crystals are dissolved, and exchange between Mg and Mn occurs within the disc during its formation. Diamagnetic MgII doping insulates the magnetic exchange between the central MnIII and those in the outer ring, thus giving an overall antiferromagnetic exchange interaction between nearest-neighbors of the outer ring. The work reveals the underlying rule for site-preference of main group metal versus transition metal in disc-like Brucite-structured cluster and provides an elegant new avenue to assemble heterometallic clusters in a stepwise fashion.