To date, small‐molecule dye–based probes have been at the forefront of research in biomedical imaging, especially in the second near‐infrared (NIR‐II) window (1.0–1.7 µm). However, how to precisely regulate the synthesized size of NIR‐II organic dye–based probes remains challenging. Moreover, systematic studies on whether the size of NIR‐II probes affects optical/pharmacokinetic properties are still rare. Here, an ingenious PEGylation strategy is developed to regulate the self‐assembly size of organic dye–based (CH1055 scaffold) NIR‐II probes (SCH1–SCH4) from nanoparticles to the single molecule, and the relationship between their size and chemical/physical properties is thoroughly investigated. Based on their own merits, nanoprobe SCH1 (≈170 nm), with outstanding fluorescent brightness (quantum yield ≈0.14%), performs accurate tracing of the lymphatic system as well as identification of vessel networks in mice brains with excellent signal‐to‐background ratio images. Meanwhile, rapidly excreted SCH4, showing fast and high passive liver tumor uptake and promising tumor/normal tissue ratios (>7), is capable of facilitating precise image‐guided tumor surgery, and also demonstrates the first example of the assessment of liver fibrosis in the NIR‐II window.