Thrombosis, a common underlying mechanism of myocardial infarction, ischemic stroke, and venous thromboembolism, is the leading cause of death in patients. Owing to their lack of targeting ability, short half-life, low utilization rate, and high risk of bleeding side effects, the current first-line thrombolytic drugs are unable to meet the requirements for effective treatment of thrombi. Photothermal therapy (PTT) represents a promising thrombolytic modality due to its precise spatiotemporal selectivity and minimal invasiveness. However, the efficacy of PTT is constrained by the limited penetration depth of conventional wavelengths, low energy conversion efficiency, and suboptimal performance of photothermal agents. Recent advancements have demonstrated that near-infrared (NIR)-mediated photothermal conversion nanomaterials exhibit significant advantages in treating thrombotic diseases. These NIR-mediated nanomaterials can rapidly convert light energy into heat via the Landau damping effect, achieving deeper tissue penetration without inducing damage, thereby enhancing the effectiveness of photothermal thrombolysis. Moreover, the modifiable nature of these nanomaterials facilitates the targeted aggregation of thrombolytic drugs at the site of thrombosis, enabling specific and effective therapy. In this review, we systematically summarize recent advances in photothermal nanomaterials with potential therapeutic applications for thrombus treatment. Specifically, we focus on composite photothermal nanomaterials that incorporate multiple components in the construction of nanocarriers. We highlight the modification technologies that utilize specific targeting ligands for enhanced thrombus treatment and the application strategies of biomimetic nanomaterials in antithrombotic therapy. Additionally, we discuss combined thrombolytic approaches such as light-triggered nitric oxide release, thrombolytic drug loading, and photodynamic therapy integration. These methods can help mitigate the risk of secondary microvascular embolization, which is crucial for comprehensive thrombus management. Collectively, these strategies offer novel insights into the treatment of thrombotic diseases.