Cancer phototherapy has been introduced as a new potential modality for tumor suppression. However, the efficacy of phototherapy has been limited due to a lack of targeted delivery of photosensitizers. Therefore, the application of biocompatible and multifunctional nanoparticles in phototherapy is appreciated. Chitosan (CS) as a cationic polymer and hyaluronic acid (HA) as a CD44-targeting agent are two widely utilized polymers in nanoparticle synthesis and functionalization. The current review focuses on the application of HA and CS nanostructures in cancer phototherapy. These nanocarriers can be used in phototherapy to induce hyperthermia and singlet oxygen generation for tumor ablation. CS and HA can be used for the synthesis of nanostructures, or they can functionalize other kinds of nanostructures used for phototherapy, such as gold nanorods. The HA and CS nanostructures can combine chemotherapy or immunotherapy with phototherapy to augment tumor suppression. Moreover, the CS nanostructures can be functionalized with HA for specific cancer phototherapy. The CS and HA nanostructures promote the cellular uptake of genes and photosensitizers to facilitate gene therapy and phototherapy. Such nanostructures specifically stimulate phototherapy at the tumor site, with particle toxic impacts on normal cells. Moreover, CS and HA nanostructures demonstrate high biocompatibility for further clinical applications.