In this work, the amine-functionalized NaYbF4:Er nanoparticles were developed as dual-modal nanoprobes for synergistic upconversion (UC) luminescence and X-ray imaging in a single system by a simple one-step method of simultaneous synthesis and surface modification. The water-soluble NaYbF4:Er nanoparticles present excellent green and dominant red UC emissions. The in vitro cell imaging shows that the high-contrast green and intense red UC emissions can be observed from HeLa cells treated with these nanoparticles, indicating the successful labeling of HeLa cells. Moreover, the localized spectra measured from HeLa cells and background presented significant green and dominant red UC emissions with the absence of any autofluorescence, further verifying that these nanoparticles can be successfully used as ideal probes for optical UC bioimaging with high contrast and non-autofluorescence. In addition, the amine-functionalized NaYbF4:Er nanoparticles maintained low cell toxicity in HeLa cells evaluated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. More importantly, these amine-functionalized NaYbF4:Er nanoparticles can also be used as X-ray imaging, owing to the large X-ray absorption efficiency of the Yb ion. The synergistic in vivo UC and X-ray imaging present significant UC luminescence and X-ray signals in the same region of a nude mouse, and the two signals are matched very well, which provides direct evidence for simultaneous UC luminescence and X-ray imaging in a single compound of lanthanide-doped material. Moreover, ex vivo UC imaging shows that these nanoparticles are first accumulated in the lung and gradually translocated from the lung into the liver. These results demonstrate that the amine-functionalized NaYbF4:Er nanoparticles presented here are very attractive nanoprobes for dual-modal UC luminescence and X-ray imaging with low cytotoxicity, autofluorescence free, and synergistic combination of the advantages of the two imaging modalities.