A generic and effective approach to “switch on” and enhance the two-photon fluorescence (TPF) emission of quenched TPF molecules, i.e., fluorene derivatives, is reported in terms of molecular recognition with a decoupling medium. Such a medium, in this case Bombyx mori silk, can recognize TPF molecules and inhibit the aggregation of the TPF molecules. The designed TPF molecules are 2,7-bis[2-(4-nitrophenyl)ethenyl]-9,9-dibutylfluorene (4NF) and 2,7-bis[2-(4-nitrophenyl)ethenyl]-9,9-dioctylfluorene (8NF), which exhibit suppressed TPF emission owing to molecular-stacking-led aggregation in the solid form. Due to the specific recognition between –NO2 in the quenched fluorescent molecules and –NH groups in silk fibroin molecules, the aggregated molecules of 4NF/8NF molecules are decoupled. This decoupling gives rise to a significant increase in TPF quantum yields. The mechanism is further confirmed by replacing the terminal group –NO2 in 8NF with –CH3 (in 2,7-bis[2-(4-methylphenyl)ethenyl]-9,9-dioctylfluorene; 8MF) to eliminate the possibility of molecular recognition. As predicted, in the case of 8MF the switching-on effect is eliminated. Completely new TPF silk fibers can additionally be applied in real-time 3D high-resolution TPF scaffold bioimaging.