The inner surface and outer surface of ferritin cage provide interfaces for the encapsulation and delivery of food nutrients. Traditional methods to fabricate ferritin-nutrients shell-core nanoparticle usually apply acid/alkaline pH transition, which may cause the activity loss of the food nutrients or the formation of insoluble aggregates. In attempt to tackle these limitations, a simple one-step method was utilized to prepare the red bean seed ferritin (RBF)-epigallocatechin (EGC)-chitosan nanoparticle (REC) by thermal treatment at 55 °C. Results indicated that the apoRBF was partially uncoiled with a decrease of 5.3% of α-helix content induced by 55 °C treatment, and the EGC molecules could spontaneously permeate into the inner cavity of the ferritin with an encapsulation ratio of 11.8% (w/w). Meanwhile, the thermal treatment facilitated the chitosan attaching onto the outer surface of the ferritin by electrostatic interactions with a binding constant of 4.7 × 105 M−1. Transmission electron microscope and dynamic light scattering results indicated that the REC was mono-dispersedly distributed, with a diameter of 12 nm and a hydrodynamic radius (RH) of 7.3 nm. In addition, the chitosan decorating onto the apoRBF improved the EGC stability by weakening the degradation of apoRBF against digestive enzymes in simulated gastrointestinal tract. This work is a novel attempt to fabricate shell-core nanoparticle in the encapsulation and delivery of functional molecules based on the ferritin cage in a benign condition without extreme pH changes.