A new self-assembly nanoprobe, mercaptoethylamine-modified-gold nanoparticles-Lysine-bridged-bis(β-cyclodextrins)-fluorescein (MGNPs-Lys-bis(β-CDs)-FL), based on fluorescence resonance energy transfer (FRET) was developed for determination of trypsin firstly in biological systems. With the Lys-bis(β-CDs)-FL complex as an energy donor and mercaptoethylamine (MEA)-modified gold nanoparticles (MGNPs) as an energy acceptor, the two parts assemble an efficient FRET nanoprobe through an amide bond. Trypsin is specific for the hydrolysis of amide linkages of lysine. Therefore, in the presence of trypsin, the nanoprobe is cleaved by trypsin on the binding sites of amide with good specificity and sensitivity, resulting in the fluorescence recovery of the quenched FL. The nanoprobe has good biological applicability and provides a potential assay for further clinical research of trypsin in biosystems.