The self-assembly processes of two kinds of octahedron-shaped M6L4 cages consisting of cis-protected Pd(II) complexes and organic tritopic ligands were investigated. Whether kinetically trapped species larger than the cages are produced or the M6L4 cage is assembled without the formation of such kinetic traps is determined by a balance between the rates of oligomerization and intramolecular cyclization, which is affected by slight changes in the chemical structure of the tritopic ligand. A numerical analysis of the experimental data based on a reaction network model where 249 reactions between the possible 56 species were considered revealed the self-assembly pathways of one of the two M6L4 cages.