The invention discloses a yolk-shell structure carbon ball@polyaniline composite microsphere and a preparation method thereof. The method comprises the following steps of (1) performing condensation polymerization reaction to prepare phenolic resin microspheres with the uniform particle diameter and single dispersion; (2) preparing phenolic resin microsphere@silicon dioxide composite microspheres;(3) performing high-temperature carbonization to obtain the carbon sphere@silicon dioxide composite structure microspheres; (4) performing aniline monomer in-situ polymerization on the carbon sphere@silicon dioxide composite structure microspheres to obtain the carbon ball@ silicon dioxide@ polyaniline composite microsphere structures; (5) removing silicon dioxide from the composite microspheresobtained in the step (4) through strong alkali etching reaction; obtaining the yolk-shell structure carbon ball@polyaniline composite microsphere. The big hole diameter and high specific surface areaare realized; meanwhile, certain mechanical intensity and chemical stability are realized; the reaction conditions are mild; the post treatment is simple; through the cooperated effects of carbon materials and conduction polymers, the electrochemical performance of the composite materials can be improved; the yolk-shell structure carbon ball@polyaniline composite microsphere can be applied to super capacitor electrode materials.