Flexible heterojunctions based on molecular systems are in high demand for applications in photonics, electronics, and smart materials, but fabrication challenges have hindered progress. Herein, we present an in situ approach to creating optical heterojunctions using hydration‐mediated flexible molecular crystals. These hydrated multi‐component molecular solids display strong blue emitting optical waveguides with minimal optical loss (0.005 dB/μm) and excellent flexibility (elastic modulus: 3.87 GPa). The water‐mediated process enables the molecular microwires with tunable elastic and plastic deformation, as well as reversible uptake and release of lattice water, facilitating the formation of flexible heterojunctions. Spectral analysis and theoretical modeling reveal that these microwires exhibit both photochromism and color‐tunable dual emission (fluorescence and phosphorescence), expanding their utility in photonic information encoding. Therefore, this work introduces a hydration‐mediated molecular engineering strategy for fabricating crystalline heterojunctions with on‐demand processability and controllable emission sequences, enabling optical signal manipulation at the micro/nanoscale.