We have for the first time reported 120 nm silver/iron oxide hybrid nano-popcorns with surface plasmon resonance tuned at near-infrared (NIR) range for imaging and therapeutic applications. The nano-popcorns displayed excellent photothermal thrombolytic effect and anticancer activity in a concentration-dependent manner upon NIR laser irradiation, benefiting the photothermal treatment of thrombosis and cancer. At low concentrations, the nano-popcorns exhibited relatively good reactive oxygen species (ROS) scavenging capability. Notably, the nano-popcorns exerted excellent magnetic resonance imaging (MRI) T2-signal after being sequestered within cells or binding on the surface of the thrombus, becoming a promising imaging agent for cell labeling and thrombus detection. Cytotoxicity, biodistribution studies, and histology analysis demonstrated no significant toxicity caused by the nano-popcorns. There was no long-term retention of the nano-popcorns in the mouse organs at the dose treated. These results give insight into the potential of using these nano-popcorns for diagnosis and treatment of diseases related to ROS, cancer, and thrombosis.