In this study, a magnetic graphene oxide modified with green carboxyl-based deep eutectic solvent (MGO@DES) was synthesized for the first time and employed as a highly efficient adsorbent for the magnetic solid-phase extraction (MSPE) of three estrogens in milk samples. With large specific surface, good hydrophobicity and abundant adsorption sites, MGO@DES exhibited excellent extraction performance for estrogens. The adsorption kinetic experiment revealed that 5 mg of MGO@DES reached the equilibrium of estrogen adsorption within 3 min. MGO@DES based MSPE coupled with HPLC-UV method was developed and applied to the determination of three estrogens in milk samples. Good linearity (R2 > 0.9953) was obtained in the range of 1–200 ng mL−1 and the low limits of detection were 0.20–0.28 ng mL−1. The spiked recoveries were in the range of 90.3–105.7%, with RSDs less than 7.9%.