Targeting drugs at mitochondria may provide an effective means of inducing cell death for cancer therapy. Here, we introduce a conjugate of a dual-ligand-modified N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer with α-tocopheryl succinate (α-TOS) (P-TOS-SS20-dNP2), which could simultaneously enhance cellular uptake via the cell-penetrating peptide dNP2 and implement delivery to mitochondria by means of the mitochondria-targeting peptide SS20. The results showed that co-modification with SS20 and dNP2 peptides successfully made up for the deficiencies of each peptide: copolymers singly modified with dNP2 were unable to increase their mitochondrial distribution in spite of increased cellular uptake, whereas copolymers singly modified with SS20 exhibited restricted mitochondrial targeting because of their poor uptake. The combination of these two functional peptides resulted in conspicuous cellular uptake and a 7.6-fold increase in accumulation in mitochondria in comparison with unmodified HPMA polymer–drug conjugates in vitro. Moreover, the dual-modified polymer–drug conjugate P-TOS-SS20-dNP2 exhibited the greatest increase in the generation of reactive oxygen species in HeLa cells, followed by great opening of mitochondrial permeability transition pores and a sharp reduction in the mitochondrial membrane potential. This further led to superior cell apoptosis in comparison with singly or non-peptide-modified HPMA copolymer–drug conjugates. The results demonstrated that combining a mitochondria-targeting peptide and a cell-penetrating peptide would substantially increase the distribution of HPMA copolymers in mitochondria, which implied an efficient strategy for promoting mitochondrial targeting efficiency.