In this work, we carried out theoretical investigation on the charge-transporting nature of 4,11-bis-[(triisopropylsilanyl)-ethynyl]-2-thia-1,3-diaza-cyclopenta[b]anthracene (1) and 4,11-bis-[(triisopropylsilanyl)-ethynyl]-2-selena-1,3-diaza-cyclopenta[b]anthracene (2) by Marcus theory and first-principle band structure. The character of the frontier molecular orbitals, reorganization energies, transfer integrals and band structures are considered in detail. The results show that the compounds 1 and 2 are ambipolar material, both electron and hole are favor of transporting. The intermolecular p-p ineraction and S···N/Se···N interaction provide the holes and electrons transport channels. The introduction of Se atom can effectively reduce the reorganization energy and considerably improve... the electron transfer integrals, thus 2 is found to be a good candidate for ambipolar semiconducting material with high mobility and balanced transport.