Protein aggregation and misfolding are the main causes of neurodegenerative diseases. The development of a sensitive detection method and early diagnosis is significant for the prevention, diagnosis and treatment of these diseases. Herein, boron dipyrromethene (BODIPY)-modified probe based on plasmon-enhanced fluorescence (PEF) was developed for the detection of amyloid-β protein (Aβ) aggregates. Gold nanoparticles (Au NPs) and BODIPY were as the plasma, fluorescent substance, respectively. Meanwhile, the distance between the Au NPs and the BODIPY was controlled by silica spacer. Compared with the original BODIPY, the fluorescence signal of BODIPY-decorated Au NPs (Au NPs@SiO2-BODIPY) exhibited 13-fold fluorescence enhancement. Three dimensions finite difference time domain (3D-FDTD) result demonstrated the signal-amplified was ascribed to the increase of electric field intensity (3.78 V/m). The linear range and detection limit for Aβ42 detection were lowered to 5–60 μM and 0.85 μM. The developed PEF probe was applied to selective and sensitive recognize Aβ aggregates in mouse colorectal carcinoma cells (CT26) and mouse pancreatic cancer cells (PAN02), which also showed a higher fluorescent signal than the original BODIPY. This method has a broad application prospect in the prediction and detection of neurodegenerative diseases.