The interfacial aggregation of three thioether-substituted phthalocyanine–magnesium(II) complexes, MgPc(SR)8, of (2,3,9,10,16,17,23,24-octakis-ethylthiophthalocyaninato)magnesium(II), [MgPc(SEt)8], (2,3,9,10,16,17,23,24-octakis-benzylthiophthalocyaninato)magnesium(II), [MgPc(SBz)8], and (2,3,9,10,16,17,23,24-octakis-benzhydrylthiophthalocyaninato)magnesium(II), [MgPc(SBh)8] were investigated in the toluene/water system by means of a centrifugal liquid membrane (CLM) method. Aggregation of MgPc(SR)8 molecules at the interface was significantly promoted by the complexation with soft metal ions such as Pd(II) and Hg(II) added to the aqueous phase. The interfacial adsorption of MgPc(SEt)8 was caused even in the absence of Pd(II) by the formation of a co-facial H-dimer, but the presence of Pd(II) promoted H-dimer aggregation at the interface. In the cases of MgPc(SBz)8 and MgPc(SBh)8, there was observed no significant self-aggregation, but in the presence of Pd(II), the interfacial aggregation of Pd(II) complexes of MgPc(SBz)8 and MgPc(SBh)8 proceeded remarkably. It was suggested that MgPc(SBz)8–Pd(II) and MgPc(SBh)8–Pd(II) could not form H-aggregates, because of the steric hindrance of benzyl or bezhydryl group, but they formed J-aggregates. Furthermore, MALDI-TOF/MS spectra indicated that oligomers of MgPc(SBz)8–Pd(II) complex were formed at the liquid/liquid interface. The present study demonstrated the first example of Pd(II)-induced interfacial aggregation of phthalocyanine derivatives at the liquid/liquid interface, and suggested the possibility of controlling the aggregate structure between H- and J-aggregates by the size of peripheral substitute groups.