Precise therapy for tumors faces challenges associated with traditional methods, such as low targeting efficiency, substantial side effects, and drug resistance. As the core regulators of cellular energy metabolism and apoptosis, mitochondria exhibit considerable advantages through targeted molecular tools that precisely deliver drugs, interfere with key pathways, and activate immune responses. This article reviews the latest advancements in mitochondria-targeted molecular tools for precision tumor therapy. Modifying molecular structures or designing functionalized carriers, small molecular drugs, metal complexes, nanodrugs, and polymeric drugs can be precisely enriched in mitochondria, disrupting the mitochondrial membrane, interfering with the respiratory chain, or activating immune pathways, thereby significantly enhancing antitumor efficacy and reducing systemic toxicity. However, further optimization of the design of mitochondria-targeted molecular tools is required, and their synergistic potential with immunotherapy metabolic regulation, and mitochondrial DNA targeting warrants further exploration. The rational design of mitochondria-targeted molecular tools holds great promise for achieving precise, personalized, and low-toxicity tumor therapy.