Mitochondria are eukaryotic sub-cellular organelle that play critical roles in energy generation for life. As the morphology of the mitochondria is dramatically versatile, there is a great demand for easy-to-use tools for mitochondria imaging. Until today, many organic probes are known to target mitochondria in live-cell conditions, but many of them are suffered from continuous leaking out from mitochondria. To overcome this challenge, we developed a bifunctional BODIPY probe that selectively engaged mitochondria and spontaneously produced the chemical crosslinking by photo-activation. To systematically optimize the dual functions, we synthesized five BODIPY fluorophores and investigated their photophysical and photo-crosslinking properties by comparing series of photo-crosslinking functional groups and their modification positions in BODIPY fluorophore. Finally, we discovered not only pcBDaza-Mito selectively stains mitochondria in live-cell condition, but also it exhibited 2.3 folds increase for photo-crosslinking efficiency to mitochondria proteins. These results present that the bifunctional BODIPY probe has great merit for robust mitochondria imaging in a live cell.