Provided are a method and an apparatus for micro-hydrocyclone purification for a flue gas carbon dioxide capture system. The method comprises: performing gas-liquid micro-hydrocylone separation with ultralow pressure drop on scrubbed flue gas, to remove aerosol particulates entrained in the flue gas; performing gas-liquid micro hydrocyclone separation with ultralow pressure drop on off-gas vented from the top of an absorption column, to remove entrained aerosol particulates; performing gas-liquid micro hydrocyclone separation with ultralow pressure drop on cooled regeneration gas, to remove entrained aerosol particulates; and performing liquid-solid and liquid-liquid two-stage micro-hydrocyclone separation on a mixed amine solution lean for carbon dioxide discharged from regeneration column, to remove entrained solid particulates and machine oil. The apparatus comprises: a water scrubbing column, rotation flow separators, liquid-solid micro-hydrocyclone separator sets, a water scrubbing tank, a absorption column, a regeneration column, liquid-solid micro-hydrocyclones and liquid-liquid micro-hydrocyclones.