A three dimensional scaffold having a three dimensional structure is easily fabricated by employing a lithography process used in a semiconductor manufacturing process. A method of fabricating the same is also disclosed have a conformational structure. In the method of fabricating a three dimensional scaffold having the conformational structure according to the present invention, a first pattern is first formed on a substrate by using a first photoresist through a lithography process, and a temporary photoresist is coated on a whole surface of the substrate. Next, a temporary pattern exposing the upper part of the first pattern to the surface is formed by using the lithography process, and a second photoresist contacting the first pattern via the temporary pattern is coated on the whole surface of the substrate. Subsequently, the temporary pattern is removed after exposing and developing the second photoresist, and then, a second pattern connected to the first pattern is formed with the second photoresist, to thereby obtain the three dimensional scaffold. Accordingly, the present invention can readily fabricate a three dimensional scaffold having a three dimensional structure through a lithography process using a photoresist.