Two photo/thermal responsive donor–acceptor molecular systems have been designed and synthesized based on interpenetrating metal organic frameworks (MOFs). For compound 1 [Zn­(CPBPY)­(HBTC)]·H2O, the formation of a 4-fold interpenetrating diamond structure displays reversible photochromic behavior upon light/heat stimuli with an offset π stacking figure for the donor carboxylate and acceptor viologen units. By comparison, the 2-fold parallel interpenetrating framework in compound 2 [Zn2(CPBPY)2(BTEC)]·2H2O·2CH3CH2OH exhibits photo coloration and thermal coloration behaviors accompanying long-lived charge separation upon light/heat stimuli with a face-to-face π-stacking figure for the donor carboxylate and acceptor viologen units. A faster response rate and stable charge separation status are observed in the system of 2 due to its large π-conjugation molecular system formed by the sandwich type π–π stacking structure. This example of structure-controlled photoresponsive systems shows a way to drive toward tuning functional system features via the design of a molecular self-assembly approach.