We demonstrate a strategy to asymmetrically introduce a Zn²⁺ chelator (MeO-DPEN) and a mitochondrial-targeting group (TPP) at the N-positions of both lactam moieties of diketopyrrolopyrrole (DPP) fluorophore. And two probes DPP-Mito and DPP-C2 were reported for the comparative studies. Both probes showed almost nonfluorescent due to the photo-induced electron transfer (PET) process from MeO-DPEN to DPP fluorophore. Upon an addition of Zn²⁺, the fluorescence intensities of both probes increased approximately 77-fold. Both probes exhibited a high binding constant, pH insensitivity, and high metal ion selectivity. The HeLa cell fluorescence imaging studies demonstrated that both probes were low toxicity and could monitor the changes in the intracellular Zn²⁺ concentrations. The confocal microscopic study showed that DPP-Mito specifically localized in mitochondria, while DPP-C2 was not organelle-specific.