Proton effects on an intramolecular donor-acceptor molecular system 4',5'-diaza-9'-(4,5-dalkylthio- 1,3-dithiol-2-ylidene)fluorenes (methylthio = L-1 (1), ethylthio = L-2 (2)) have been experimentally and theoretically studied. Structures of L-2 (2) and three protonated salts, [L-2 center dot H]CF3SO3 (3), [L-1 center dot H]CF3SO3 (4), and [L-1 center dot H]ClO4 (5), were characterized by single-crystal X-ray determination. In all these salts the cations are found to be monoprotonated even in an excessive amount of acid. The protonated imine group forms strong N-H center dot center dot center dot O or N-H center dot center dot center dot N hydrogen bonds, which enhance the interaction between cations and anions and play an important role in the molecular packing. The measurement of UV-vis spectra indicates a two-step red shift of the absorption bands, which corresponds to the two-step protonation of L in solution. The intramolecular charge-transfer (ICT) property is enhanced when the compounds are protonated. Compound L is also a proton sensible fluorescent system with two-step remarkable changes in band energy and intensity. The study on the effect of protonation is further complemented by theoretical calculation with the DFT/TDDFF method.