The pigments composition and structure of the mural painting at Pongjongsa Kuknakjon is discussed. The structure of inner wall is consisited of Paint layer, Ground divided two layers of yellow and white pigments, Support. In case of outer wall, it is consisted of Paint layer, Ground divided three layers of yellow and green pigments, a layer mixed green pigments and paint layer, Support. As a result of compositon analysis of mural painting pigments at Pongjongsa Kuknakjon using Micro-area X-ray diffraction system, the red pigment on inner wall is consisted of Heamatite($Fe_2O_3$), Magnetite($Fe_3O_4$)of deep black pigment, and Chalcocite($Cu_2S$) of light black pigment. The white pigment on outer wall is consisted of Anglesite($PbSO_4$) and Atacamite($Cu_2CI(OH)_3$) of green pigment. We found out that natural pigments painted in the mural painting at Pongjongsa Kuknakjon has kept up its own color for a long time due to using the natural pigment not to artificial synthetic pigment.