Cancer treatment has traditionally relied on surgical intervention, chemotherapy, and radiation therapy; however, these procedures often result in significant side effects, such as compromised immune function and cellular health. The emergence of drug resistance further complicates chemotherapy and necessitates the exploration of alternative therapeutic approaches. Photothermal therapy (PTT) presents a promising non-invasive cancer treatment modality that uses photothermal agents (PTAs) to convert light energy into localized heat, selectively targeting and eradicating tumor cells. This review highlights the potential of organic dyes-based PTTAs in cancer treatment due to their biocompatibility, photostability, and robust absorption in the near-infrared (NIR) region. These dyes exhibit high photothermal conversion efficiency (PCE), especially in the NIR-II window (1000–1700 nm), and deep tissue absorption, rendering them suitable for medical applications. This study also examines the interplay between key photophysical processes (fluorescence, vibrational relaxation, and intersystem crossing) that govern the efficacy of PTT and photodynamic therapy (PDT). The molecular structure of organic dyes and their role in multimodal cancer therapy are discussed in detail, with emphasis on optimizing the balance of photothermal efficiency and biocompatibility. Through a comprehensive review of recent advances in dyes, this review sheds light on the development of next-generation PTTAs, facilitating their integration in oncology.