To enhance the pore structure of green coffee beans (GCB) and detect the sorption capacity and extraction characteristics of flavor compounds before roasting, this study employed several methods: hot air drying (HD), freeze-drying (FD), 3-levels short-time heating with puffing (SH₁P, SH₂P, and SH₃P), and 3-levels microwave with puffing (MW₄₅P, MW₆₀P, and MW₇₅P). These methods were applied to GCBs pre-soaked in water for different times. The effects of these treatments on color change, porosity, microstructure, citric acid sorption capacity, and caffeine and chlorogenic acid extraction yield were investigated. Results indicated that, except for GCBs treated with SH₁P, SH₂P, SH₃P, and MW₇₅P, all other modified GCBs showed minimal color change. GCBs treated with MW₆₀P exhibited favorable pore structures. MW₆₀P treatments significantly improved the extraction yield of caffeine and chlorogenic acid. Furthermore, the increased porosity and improved pore size distribution of GCB after MW₆₀P resulted in a significant increase in the sorption of citric acid onto modified GCB. The rate of the sorption reaction followed the pseudo-first-order kinetics. In conclusion, MW₆₀P are effective treatments for enhancing the microstructure of GCB, improving sorption capacity, and improving the extraction yield of flavor compounds.