As an emerging class of hybrid materials, donor-acceptor (D-A) hybrid crystals with photoactive organic and inorganic components have gradually become an ideal platform for photochromic materials. Wherein the most available organic components are electron-poor naphthalenediimide, pyridinium, and triazine derivatives, inorganic units are electron-rich polyoxometalates and metal halides. Herein, we introduced pyridinium moieties into the naphthalenediimide core by conjugated bonds so as to increase the electron deficiency of organic species for enhanced photochromic properties. Four anion-π interaction directed hybrid crystals, (Me2DPNDI)3·(PW12O40)2 (1), (Et2DPNDI)3·(DMSO)2·(PMo12O40)2 (2), (Et2DPNDI)3·(PW12O40)2 (3), and (Et2DPNDI)2·(SiMo12O40) (4), have been obtained, which possess reversible, naked-eye perceptible color changes with varying light response rates. These rates are as follows: 3 > 1 > 4 > 2. As expected, such D-A hybrid crystals with conjugated naphthalenediimide-pyridinium salts feature both photo- and thermally induced electron transfer pathways, along with enhanced anion-π interactions. Consequently, they demonstrate a higher rate of photochromism compared to those of hybrids containing naphthalenediimide or pyridinium derivatives as organic acceptors.