A micro-column hydrophilic interaction chromatographic(μ-HILIC) method was developed for the determination of microcystins(MC-LR,MC-YR,and MC-RR).The effects of composition of the mobile phase,the flow rate of the mobile phase,concentration of the buffer system and pH value on the separation of microcystins were all investigated.The results show;The separation is performed with a gradient elution of mobile phase A(10 mmol/L ammonium acetate buffer pH 6.8) and mobile phase B(acetonitrile).The standard sample can be separated in base line with in 8 mins.The detection limit(S/N =3) of the method is found to be 0.10 mg/L.RSD's(n = 5) is≤2.3%,and the average recovery obtained is≥86.2%.Compared with the traditional reverse-phase HPLC,this new study shows an advantage in the predigesting of the mobile phase,operating conditions of the experiment and rapid detection of the peak signal.