CH4@C60 was the first example an organic molecule has been embedded in C60, and by far the largest molecule. CH4 can rotate freely in the molecular cage, and the carbon skeleton structure of the C60 has no obvious deformation. The electronic structure of CH4@C60 and interaction between C60 and CH4 were studied using quantum mechanical calculation method. The different reaction sites on C-C bonds in C60 and the weak Van der Walls interaction between CH4 and C60 were shown clearly. These results and the orbital interaction between CH4 and C60 were helpful for understanding and further application of this unique biggest organic molecule CH4 contained in C60 structure so far.