A combined method of the time-dependent density functional theory (TDDFT) and sum-overstate (SOS) formula was implemented to model multiphoton absorption spectra, including two-photon absorption (2PA) and three-photon absorption (3PA), of Sc2C2@C-68 and Sc3N@C-68 endohedral metallofullerenes (EMFs). This method has been proved to be effective by comparisons between the calculated and experimental results of trans-4,4'-bis[diphenylamino]stilbene. It was found that the multiphoton absorption cross sections were larger for Sc2C2@C-68 than that of Sc3N@C-68. The electronic origin of multiphoton absorption has been identified with respect to the molecular orbitals involved in charge transfer process. It shows that the increase of pi-charges on the cage Of C-68 results in a large multiphoton absorption cross section in EMFs.