The fast development of the design, construction, and application of metal–organic materials including infinite metal–organic frameworks (MOFs) and discrete metal–organic cages (MOCs) has not only propelled the advance of modern supramolecular syntheses to an unprecedented level, but also burgeoned various kinds of detection and characterization technologies. Herein, complementary techniques, including diversified NMR and ESI‐MS spectrometry, solid‐state crystallography, and theoretical simulation are exploited to elucidate the structural evolution of a dynamic supramolecular coordination system involving PdII–MOCs of different compositions. The combination of various kinds of modern techniques verifies the anion template effect, which leads to the preferred formation and further conversion of Pd2L4 or Pd3L6 cages.