One-photon absorption and two-photon absorption (TPA) properties of three tris(picolyl)amine-based zinc ion sensors are investigated by employing the density functional response theory in combination with the polarizable continuum model. The different isomer and coordination geometry of each probe are taken into account. Special emphasis is placed on the effects of isomerism and the coordination mode on the optical properties. The intra-molecular charge transfer (ICT) properties are specified by natural bond orbital charge analysis. It is shown that the isomerism has non-negligible effects on TPA properties of free ligands. It is found that both the TPA wavelength and the cross section are highly dependent on the coordination mode. When the zinc ion connects with the picolyl unit in the middle of a ligand, the zinc complex has a large TPA intensity in a long wavelength range due to the increased ICT mechanism.