Background: Phellodendron chinense Schneid is an important Chinese herb that contains berberine, phellodendrine, palmatine, and medicinal compounds. The germination rate of Phellodendron chinense Schneid seeds is lower after storage, and the exogenous gibberellin3 (GA3) hormone promotes seed germination, but the mechanism is not cleared. Results: Exogenous GA3 hormone promoted germination of Phellodendron chinense Schneid seeds, elevated germination rates. It also increased the levels of activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Moreover, it enhanced the contents of berberine and endogenous GA3, and increased the expression levels of Pc(S)-GA2ox, Pc(S)-GA3ox, and Pc(S)-THBO. However, it reduced the expression level of Pc(S)-ABI5. Furthermore, exogenous GA3 up-regulated the protein levels of DNA guides RNA polymerase β'-subunits, Coffee coenzyme A oxymethyl transferase, and Histone H1. Conclusion: These findings indicated that exogenous GA3 promoted germination of Phellodendron chinense Schneid seeds by regulating the expression levels of phytohormone related genes and anabolic proteins.