A micro-separator for gas chromatography includes a base substrate having a trench defining a micro-column, and a three-dimensional (3D) porous ceramic-polymer composite disposed in the micro-column and having pores that three-dimensionally connected to each other with periodicity. The 3D porous ceramic-polymer composite includes a ceramic nano-structure, which forms an array of three-dimensionally arranged nano-shells, and a reaction-activating layer combined on a surface of the ceramic nano-structure and including a polymeric reaction-activating material. A thickness of the 3D porous ceramic-polymer composite is 10 μm to 20 μm, a column length of the 3D porous ceramic-polymer composite is 30 cm to 70 cm, and a shell thickness of the ceramic nano-structure is 20 nm to 60 nm. The micro-separator may have improved separation performance and durability.