Noninvasive visualization of deep tissue lymphatic metastasis is crucial for diagnosing malignant tumors and predicting prognosis. However, the limited diffusivity and specificity of imaging contrast agents that are transported in lymph vessels (LVs), even for those agents delivered by nanocarriers, make long-distance tracing of the lymphatic system in vivo challenging. Here, we develop a computed tomography (CT)/fluorescence dual-modality phospholipid nanoprobe (PL(I/D)NP) with a negative charge and sub-60 nm size. By using micro-CT, we noninvasively traced the LVs from the subcutaneous injection site in feet to the thoracic ducts with an entire length of ∼68 mm and measured the volume of the lymph nodes (LNs) and their separation distance along the LVs. For diagnostic imaging of tumor lymphatic metastasis, all LNs with metastasis were identified in vivo. Thus, with their long-distance diffusivity, high lymphatic capillary specificity, and quantifiability, the PL(I/D)NPs combined with noninvasive imaging accurately depicted the changes in the lymphatic system under pathologic conditions, especially cancer metastasis, which indicates their high potential for clinical applicability.