The linear and nonlinear optical properties of two BODIPY derivatives, 1,7-Diphenyl-3,5-bis(9,9-dimethyl-9H-fluoren-2-yl)-boron-diuoride-azadipyrromethene (ZL-61) and 1,7-Diphenyl-3,5-bis(4-(1,2,2-triphenylvinyl)phenyl)-boron-diuoride-azadipyrromethene (ZL-22), were comprehensively investigated based on experimental and theoretical studies. It was found that both compounds show a strong two-photon absorption response in the near-infrared regime, and the two-photon-absorption cross-section values of ZL-61 and ZL-22 were determined to be 8321 GM and 1864 GM at 800 nm, respectively. The improvement of the two-photon absorption cross section in ZL-61 was attributed to the enhancement of the donor group, which was confirmed by transient absorption measurements and DFT calculation. Our results indicate that these BODIPY derivatives are a promising candidate for optical limiting and two-photon imaging applications.