Faster and more convenient construction of different functional multi-input–multi-output molecular logic devices has become a current research hotspot. In this study, a complex was synthesized using bovine serum albumin (BSA) and hydrazide dihydroxydisalicylaldehyde by a combinatorial approach. Then, the interaction mechanism was investigated by fluorescence spectroscopy and molecular simulation. Both methods revealed that the interaction between BSA and hydrazide dihydroxydisalicylaldehyde mainly occurred at site I of BSA. The main types of interactions included hydrogen bonding and van der Waals forces. Based on hybridized fluorescence resonance and electron exchange energy transfer, the complex generated two fluorescence emission peaks. Then, a digital comparator and a molecular logic circuit were designed using different metal ions or pH to modulate the output signals. Notably, the apparent increase in the fluorescence lifetime of the donor serves as an important basis for electron exchange between the donor and the acceptor.