Photoacoustic imaging (PAI) and imaging-guided photothermal therapy (PTT) in the second near-infrared window (NIR-II, 1000-1700nm) have received increasing attention owing to their advantages of greater penetration depth and higher signal-to-noise ratio. Plasmonic nanomaterials with tunable optical properties and strong light absorption provide an alternative to dye molecules, showing great prospects for phototheranostic applications. In this review, the research progress in principally modulating the optical properties of plasmonic nanomaterials, especially affecting parameters such as size, morphology, and surface chemical modification, is introduced. The commonly used plasmonic nanomaterials in the NIR-II window, including noble metals, semiconductors, and heterostructures, are then summarized. In addition, the biomedical applications of these NIR-II plasmonic nanomaterials for PAI and PTT in phototheranostics are highlighted. Finally, the perspectives and challenges for advancing plasmonic nanomaterials for practical use and clinical translation are discussed.