Developing dynamic encryption materials with time‐dependent outputs has gained importance in the digital age. While many studies have introduced phosphorescent, polymeric, and/or self‐assembled materials for this purpose, challenges such as poor handleability, short readout duration, and single‐mode output persist. To address these issues, designed three photochromic molecules—DAE‐B, DAE‐NH, and DAE‐N with different photoisomerization rates are designed. Under 254 nm irradiation, DAE‐B and DAE‐NH appear magenta per cyclization, while DAE‐N emits orange fluorescence. Notably, DAE‐B and DAE‐NH are visible under both visible light and UV light (254 and 365 nm), whereas DAE‐N is visible only under UV light. Leveraging these properties, a time‐dependent dynamic encryption system using DAE‐B and DAE‐NH is developed, where the correct message is accessible only at a specific time, while wrong information would appear at other time points. Additionally, by integrating DAE‐B, DAE‐NH, and DAE‐N into QR codes (quick‐response code), and combining this with the scanning sequence, time, and wavelength, a dual‐mode, 3D encryption system that operates under both visible and UV light is created. This innovation not only advances time‐based encryption techniques but also contributes to the development of molecular clock‐based encryption materials.