The reaction of hexachlorocyclotri(λ5-phosphazene), N3P3Cl6, with a series of pyrimidine-2-thiol in the presence of triethylamine in boiling tetrahydrofuran solution affords only a geminal isomer, N3P3(N-S)2Cl4 (N-S = 2-pyrimidinylthio (pms), 4,6-dimethyl-2-pyrimidinylthio (dmpms), and trifluoromethyl-2-pyrimidinylthio (fmpms)) in high yield. The molecular structures of N3P3(pms)2Cl4 (monoclinic P21/n, a = 7.686(2), b = 28.236(7), c = 8.760(2) Å, β=99.87(2)̊, V = 1873.2(8) Å3, Z = 4, R = 0.052) and N3P3(dmpms)2Cl4 (triclinic P1̄, a = 8.698(3), b = 9.630(3), c = 14.179(6) Å, α = 100.88(3), β = 92.83(3), γ = 103.84(3)°, V = 1126.9(7) Å3, Z = 2, A = 0.049) have been solved. The crystal structures disclose that the nitrogen atom of the 2-pyrimidinylthiol group significantly interacts with the phosphorus atom of the cyclotri(phosphazene) ring within the sum of the van der Waals radii (3.40 Å). The P⋯N intramolecular interaction of N3P3(dmpms)2Cl4 (P(1)-N(5), 3.109(4); P(1)-N(7), 3.126(4) Å) is considerably longer than that of N3P3(pms)2Cl4 (2.965(7), 2.986(7) Å). Although such a unique intramolecular interaction does not seem to be exactly retained in solution, the steric effects of the geminal bis-substituted ligands seem to hinder further substitution at other untouched phosphorus atoms. The formation of only a geminal isomer and its structure seem to be involved in the mechanism of the substitution reaction.