A highly sensitive method using reduced graphene oxide with iron oxide (rGO/Fe3O4) as the sorbent in magnetic SPE has been developed for the purification of five anthraquinones (emodin, rhein, aloeemodin, physcion, and chrysophanol) in rhubarb and rat urine by ultra-HPLC coupled with quadrupole TOF/MS. The extraction was accomplished by adding trace amount rGO/Fe3O4 suspension to 200 mL of aqueous mixture, and the excellent adsorption capacity of the nanoparticles was fully demonstrated in this procedure. Under the optimized conditions, the calibration curves were linear in the concentration range of 0.05-27.77 ng/mL with correlation coefficients varying from 0.9902 to 0.9978. The LODs ranged from 0.28 to 58.99 pg/mL. The experimental results indicated that the proposed method was feasible for the analysis of anthraquinones in rhubarb and urine samples.