• Two isomeric metal-organic frameworks are prepared based on naphthalenediimide and naphthalenedicarboxylic acid. • Complexes 1 and 2 exhibit different photochromism and photocontrolled luminescence upon UV–Vis light irradiation. • Noncovalent interactions play an important role in the photochromic properties of MOFs. As a class of special type materials, photochromic metal-organic frameworks (MOFs) have attracted extensive attention because their usually show interesting color changes and coupled with the variation of some chemical and physical properties under light irradiation. In order to study the effect of secondary building on the photochromism of MOFs, two isomeric naphthalenediimide-based MOFs with different secondary building linkers, namely [Zn 2 (DPNDI)(2,6-NDC) 2 ] ( 1 ) and [Zn 2 (DPNDI)(1,4-NDC) 2 ] ( 2 ) (DPNDI = N, N ’-di(3-pyridyl)-1,4,5,8-naphthalenediimide, 1,4-H 2 NDC = 1,4-naphthalenedicarboxylic acid, 2,6-H 2 NDC = 2,6-naphthalenedicarboxylic acid), were synthesized via solvothermal reaction and the structure were characterized by single-crystal X-ray diffraction, IR and TGA. Owing to the different C H···π interactions between the naphthalene moieties of dicarboxylic acid and electron-deficient DPNDI ligand, they showed different photochromic behaviors and photocontrolled luminescence upon ultraviolet-visible irradiation. Specifically, complex 2 was photochromic but complex 1 was not. The difference can be ascribed to the larger C H···π interaction in complex 1 than in complex 2 . This work is expected to provide a new perspective for designing novel photochromic MOF materials Two isomeric naphthalenediimide-based MOFs with different secondary building linkers have been prepared, which exhibit different photochromic behaviors and photocontrolled luminescence upon ultraviolet-visible irradiation.