The present invention relates to a heat dissipating apparatus having micro-structure layer and method for fabricating the same. The method provides two highly heat conductive members having structure patterns. A highly heat conductive material is coated on the structured patterns by means of injection molding for forming a micro-structure layer. The two highly heat conductive members are assembled to form a heat dissipating apparatus having micro-structure layer. The heat dissipating apparatus comprises a main body composed of the highly heat conductive members. The main body forms an accommodating cavity, and inner surfaces of the accommodating cavity form the micro-structure layer. A working fluid is filled into the accommodating cavity for transferring heat from a heat absorbing surface to a heat dissipating surface.