Simultaneous in vivo luminescence and X-ray bioimaging in a tissue or animal integrates the advantages of each single-modal imaging technology, and will find widespread application in biological and clinical fields. However, synergistic dual-modal bioimaging that utilizes a new generation of upconversion nanoprobes is still limited. In addition, investigations concentrated on in vivo biodistribution of these nanoprobes may contribute to diagnosis and treatment, but long-term in vivo tracking based on these nanoprobes is rarely reported. In this work, water-soluble NaLuF4: Yb/Er nanophosphors were prepared through modified one-pot simultaneous synthesis and surface modification method. Owing to the outstanding upconverting emissions and large X-ray absorption coefficient/K-edge value of Lu and doped Yb ions, the obtained nanoprobes were successfully used as luminescent nanoprobes and X-ray contrast agents for in vivo synergistic upconversion luminescence and X-ray bioimaging. The in vivo biodistribution of these nanoprobes were observed, and the results based on long-term tracking reveal that the as-prepared nanoprobes first aggregated in the lung of the mouse, transferred to the liver, and finally moved to the spleen.