Near-infrared II (NIR-II) photoacoustic imaging (PAI) technology is an emerging biomedical imaging modality characterized by high spatial resolution, deep tissue penetration, and high signal-to-noise ratio. NIR-II PAI enables highly clear real-time monitoring of various physiological and pathological processes and visualizes different biological entities, making it crucial for advancements in life sciences and medicine. NIR-II PAI technology holds significant application potential in disease diagnosis and treatment, particularly in early diagnosis, precise localization, boundary delineation, and monitoring of treatment response for tumors and other conditions. By combining with multimodal or diagnostic-therapeutic integrated molecular probes, this technology enables accurate disease localization and guided treatment, which is crucial for early diagnosis and therapy. This review provides a detailed overview of research progress on NIR-II PAI probes, discussing the emergence and latest developments of various NIR-II PAI probes and their applications in early diagnosis and treatment of tumors, cerebrovascular systems, inflammation, and other tissues. Additionally, it summarizes the development status of these probes and outlines future prospects and challenges.