Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ(T)(max)). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) properties of some novel PDI and pyrene derivatives were comparatively investigated by the density functional theory (DFT) and Zerner's intermediate neglect of differential overlap (ZINDO) methods. The calculated results indicate that with respect to PDI derivatives, the maximum TPA cross-sections for pyrene compounds increase obviously, the maximum peaks of OPA and TPA spectra are blue-shifted, the ΔE(H-L) (energy gaps between the highest occupied orbital and the lowest unoccupied orbital) increase. The different π-conjugated bridges (fluorene and pyrene) and terminal groups have slight effect on the OPA properties. Nevertheless, the molecules bearing 1,6-disubstituted pyrene as the π-conjugated bridge display the largest δ(T)(max) in both series of compounds 3 and 4. Moreover, the δ(T)(max) values of molecules with benzothiazole-substituted terminal groups are larger than those of the molecules with diphenylamine, which is attributed to benzothiazole groups stabilizing the planarity of the branch parts, extending the conjugated length and increasing the π-electron delocalized extent. Furthermore, the molecular size has marked effect on OPA and TPA properties. It is worthy to mention that cruciform 8 displays the largest δ(T)(max) among all the studied molecules in the range of 600-1100 nm. This research could provide a better understanding for the origin of the linear and nonlinear optical properties, and it would be helpful to gain more information about designing two-photon absorption materials with large δ(T)(max).