The photo-induced superstructure of polymorph C of trans-[Fe(abpt)(2)(NCS)(2)] (abpt = 4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole) is discovered as a commensurate modulated structure by single-crystal X-ray diffraction under irradiation. The crystal structure at 25 K before the photo-irradiation composed of two crystallographically independent iron molecules, one of which exhibits high spin (HS) state and the other at low spin (LS) state. Under green laser light (λ = 532 nm) irradiation, the LS molecule (Fe1) is found to be excited to a metastable HS state and gives rise to a commensurate tripled superstructure along the c axis. In addition, it is confirmed that this modulation persists until the HS → LS relaxation temperature beyond 52 K. Our structural findings suggest that the structural modulation and the site-selective LS → HS excitation are highly correlated.