In this work, a double shell material chitosan (CS)-recombinant soybean seed H-2 ferritin (H-2F) was fabricated to encapsulate epigallocatechin gallate (EGCG) molecules. EGCG-loaded H-2F complex (EHF) was firstly prepared by taking advantages of the reversible self-assembly of the ferritin, and the EHF-CS composite (EHFC) was fabricated by electrostatic interactions with binding number n of (4.1 ± 0.11) and binding constant K of ((5.3 ± 0.2) × 105M−1), respectively. It was calculated that about 12.6 of EGCG molecules can be encapsulated in one H-2F ferritin cage with an encapsulation efficiency of 9.69% (w/w). SDS-PAGE analysis indicated that the CS binding to H-2F could inhibit ferritin degradation by pepsin and trypsin; the stability of EGCG molecules in EHFC was also significantly improved in simulated gastrointestinal tract. In addition, the chitosan-ferritin double shells were beneficial for the transport of EGCG across the Caco-2 monolayer model based on ferritin uptake. This work demonstrates a novel method to promote stabilization and absorption of food bioactive molecules.