Numerous cellular functions are closely reliant on mitochondria and so the capability to conduct long-term stable studies of their activity is of great importance. However, current commercial mitochondrial probes are severely limited in their ability to trace mitochondria due to their inherently poor stability. Here, for the first time, we designed a novel mitochondrial fluorescent probe using InP quantum dots (QDs) as a fluorescent master and skillfully combined with (3-carboxypropyl)triphenylphosphine (TPP) for specific recognition. The bespoke InP QDs probes described here exhibited clear advantages, including simple and low-cost synthesis, high quantum yields, extremely low toxicity, good biocompatibility, and excellent photochemical stability, thus representing a versatile, novel mitochondrial fluorescent probe, particularly suitable in applications traditionally undertaken by Cd-based QDs in biological fields.