A novel FeIII complex [Fe(Hex-tnal)2]BPh4 (1) with a tridentate N2O ligand having an n-hexyl chain, Hex-Htnal (=1-((((1-hexyl-1H-1,2,3-triazol-4-yl)methyl)imino)methyl)naphthalen-2-ol), is reported. Temperature-dependent magnetic susceptibility measurements revealed that 1 exhibits a two-step spin crossover (SCO) transition in the 400-10 K temperature range, including an unusual gradual χMT change above RT (300-345 K) and a hysteretic χMT jump in a narrow temperature range of 345-357 K. These behaviors were also characterized by differential scanning calorimetry. Variable-temperature single-crystal X-ray diffraction studies revealed that the order-disorder transition and conformational change of the hexyl chains and the symmetry change associated with the re-entrant structural phase transition, namely triclinic P1̄ (100-275 K) ↔ monoclinic C2/c (296-340 K) ↔ triclinic P1̄ (360 K), are coupled to variations in intermolecular interactions and the N4O2 coordination environment, resulting in the occurrence of the unusual two-step SCO transition of 1. This study demonstrates that the flexible motion of alkyl substituents in the supramolecular lattice influences the occurrence of anomalous magnetic switching properties.