The complexes of epigallocatechin (EGC) and 5-hydroxymethylfurfural (5-HMF) were respectively constructed in water-soluble and ethanol-soluble systems to study the reducing effect of EGC on harmful substance 5-HMF in food. The results showed that EGC and 5-HMF can be combined by non-covalent way in water-soluble and ethanol-soluble systems, and the main force were hydrogen bond. Scanning electron microscope, X-ray diffractometer and differential scanning calorimeter displayed that EGC combined with 5-HMF in the form of co-amorphous complexes. Fourier transform infrared spectroscopy, 1H-NMR spectroscopy and molecular dynamics simulation confirmed that EGC can form O–H⋯O hydrogen bonds with adjacent 5-HMF molecules. Thin-layer chromatography and in vitro digestive juice assay further proved that no free 5-HMF were observed after EGC and 5-HMF formed complexes. The results indicated that EGC and 5-HMF can form an EGC-5-HMF co-amorphous complexes through intermolecular hydrogen bonding, thereby changing the stability of free 5-HMF. EGC has favorable potential for the control of 5-HMF in food.