The invention discloses a synthesis method of guanidine organic magnetic ionic liquid, in particular guanidyl cation-based organic magnetic ionic liquid. The synthesis method is technically characterized in that chloroalkane or bromoalkane, 1,1,3,3-tetramethyl guanidine, sodium hydroxide or potassium hydroxide, a 4-hydroxy-2,2,6,6-tetramethyl piperidine oxide and chlorosulfonic acid are used as raw materials to synthesize a series of paramagnetic organic magnetic ionic liquid, and the structural formula is as shown in formula (I) shown in the description. The compound is novel in structure and can form aqueous two phase with inorganic salt (potassium phosphate, dipotassium phosphate, potassium carbonate, sodium carbonate, ammonium bisulfate, sodium sulfate and the like); an aqueous two phase system of the magnetic ionic liquid is internationally developed for the first time. Compared with the traditional aqueous two phase system, the aqueous two phase system of the magnetic ionic liquid is capable of accelerating the separation of two phases through an applied magnetic field assisted manner, so as to improve the phase separation efficiency. The system has wide potential purposes, and has unique advantage in the fields of extraction, micro-extraction, separation and analysis.