The present invention relates to a system for remediating highly contaminated fine soil using multiple micro hydrocyclones that includes: a mill adapted to mix contaminated soil with water and to individualize the soil; a screen adapted to separate the soil introduced from the mill into soil having given particle sizes; a separator adapted to finely separate the soil having particle sizes of less than a given value by particle size from the soil having the given particle sizes separated through the screen; a remediating unit adapted to wash the finely separated soil introduced from the separator by particle size by means of process water for washing; and a filtering unit adapted to separately discharge the soil washed and introduced through the remediating unit and the process water for washing contained in the soil.