The molecular binding behavior of three sulfonated calixarene hosts, p-sulfonatocalix[4]arene (SC4A), p-sulfonatocalix[5]arene (SC5A), and p-sulfonatothiacalix[4]arene (STC4A), with two phenanthroline-diium guests, 5,6-dihydropyrazion[1,2,3,4-lmn][1,10]phenanthroline-4,7-diium (DP²⁺) and 6,7-dihydro-5H-[1,4]diazepino[1,2,3,4-lmn][1,10]phenanthroline-4,8-diium (PPQ²⁺), were systemically investigated in neutral phosphate buffer solutions by microcalorimetry, cyclic voltammetry, NMR spectroscopy, and molecular mechanics calculation. We found that the phenanthroline-diium guests were captured by SC4A, SC5A, and STC4A from their aromatic moieties. Furthermore, STC4A displays a high affinity with phenanthroline-diium guests in the order of magnitude of 10⁵ M⁻¹. It is the reported highest binding order of magnitude for STC4A up to now, although the binding constants of SC4A and SC5A with phenanthroline-diium guests are still a little larger.