The vacancies in the semiconductor nanocrystals not only induce unique properties, but also provide spaces for engineering them with multifunctions by the introduction of other elements. Herein, the vacancy of Cu2−xSe nanoparticles was tuned by doping with magnetic ferric ions (Fe3+) at room temperature, and the position and intensity of the near-infrared localized surface plasmon resonance (LSPR) in the resultant nanostructure can be finely controlled by altering the feeding amount of Fe3+ ions. The results of the density-functional theory (DFT) calculations show that both doping and replacement reactions are favourable. Owing to its tunable near-infrared absorption and magnetic property, the obtained hybrid nanostructure was demonstrated to be a novel nanotheranostic agent for effective deep-tissue photoacoustic imaging, magnetic resonance imaging, and photothermal therapy of cancer.