As a semi-autonomous organelle, the eukaryotic mitochondrion possesses an individual DNA and protein synthesizing system. Therefore, the mitochondrial DNA-targeting probes are powerful tools to understand the functions in physiological processes. Herein, we report a novel Ru(ii) complex (HLRu) based on a phenanthroline derivative to target mitochondrial DNA. The nonlinear optical property study revealed a reverse nonlinear optical refraction character from self-focusing to self-defocusing response before and after complexation with Ru(ii). Furthermore, the two-photon absorption and high biocompatibility of complex HLRu highlight its potential applications in biological processes. It was found that complex HLRu specifically binds to mitochondrial DNA in living cells and enables imaging of tissues with minimal auto-fluorescence. As a result, this complex HLRu probe offers a promising platform to directly monitor mitochondrial DNA in living cells.