The incidence of skin cancer is rising worldwide, with non-melanoma skin cancer ranked as the fifth most prevalent cancer in 2022, presenting a significant burden on public health. Photothermal therapy has emerged as a promising treatment that employs near-infrared light to selectively destroy cancerous tissue. While the integration of metallic nanoparticles has demonstrated enhanced thermal performance, concerns over their low tissue clearance rate and long-term toxicity have hindered their clinical translation. Polydopamine (PDA) nanoparticles have recently garnered attention as a promising alternative due to their biodegradability and biocompatibility. This study presents a finite element-based multiscale modeling framework to investigate PDA nanoparticle-enhanced photothermal therapy for skin cancer treatment. Numerically characterized optical properties of PDA nanoparticles were incorporated into a three-dimensional, multi-layered skin tissue model that includes a region of squamous cell carcinoma. Heat transfer was simulated by coupling the Pennes’ bioheat transfer equation with the Beer–Lambert law to compute the spatiotemporal temperature distribution during laser irradiation. Model validation against experimental temperature data from PDA suspensions at various concentrations showed strong agreement. Parametric studies explored the effect of PDA nanoparticle size, concentration, laser intensity, and beam profile on temperature profiles. The results demonstrated that PDA nanoparticles increased tumor temperature compared to treatments without nanoparticles. The temperature increased by 6˚C when 1000 μg/mL was irradiated for 10 minutes with a 1.4 W/cm² laser intensity. These findings help to deepen our understanding of the thermal behavior of PDA nanoparticles in biological tissues and support their potential as a biocompatible alternative for enhanced photothermal therapy.