Gardenia jasminoides Ellis, a representative for “homology of medicine and food”, can be used to produce pigment and edible oil. Here, aqueous enzymatic extraction (AEE) combined with puffing pre-treatment was explored to prepare oil from gardenia seeds. Both wet-heating puffing (WP) at 90 °C and dry-heating puffing (DP) at 1.0 MPa facilitated the release of free oil by AEE, resulting in the highest free oil yields (FOY) of 21.8% and 23.2% within 3 h, much higher than that of un-puffed group. Additionally, active crocin and geniposide were also completely released. The FOY obtained was much higher than mechanical pressing method (10.44%), and close to solvent extraction (25.45%). Microstructure analysis indicated that gardenia seeds expanded by dry-heating puffing (1.0 MPa) had a larger, rougher surface and porous structure than other groups. Overall, AEE coupled with puffing pre-treatment developed is an eco-friendly extraction technology with high efficiency that can be employed to oil preparation.Graphical abstract: