To treat the microalgae in ship's ballast water economically and effectively,the water that contains Pyramimonas sp. and Heterosigma akashiwo is treated by the iron-carbon micro-electrolysis technique. The factors influencing the treatment efficiency are considered where the factors include the iron and active carbon dosage,iron to active carbon mass ratio,iron and active carbon particle sizes,blender's rotational speed,and reaction time. The result shows that Pyramimonas sp. removal rate can reach98. 34% under the condition of the iron and active carbon dosage 12 g / L,the mass ratio of iron to active carbon 1∶ 1,the iron particle size [0. 15,0. 90) mm,the active carbon particle size less than 0. 15 mm,the rotational speed 160 r / min and the reaction time 75 min; Heterosigma akashiwo removal rate can reach 99. 61% under the condition of the iron and active carbon dosage 12 g / L,the mass ratio of iron to active carbon 1∶ 1,both the iron and active carbon particle size less than 0. 15 mm,the rotational speed140 r / min and the reaction time 60 min.