β-NaYF(4) : Yb,Er upconversion nanoparticles (UCNPs) can emit bright green fluorescence under near-infrared (NIR) light excitation which is safe to the body and can penetrate deeply into tissues. The application of UCNPs in biolabeling and imaging has received great attention recently. In this work, β-NaYF(4) : Yb,Er UCNPs with an average size of 35 nm, uniformly spherical shape, and surface modified with amino groups were synthesized by a one-step green solvothermal approach through the use of room-temperature ionic liquids as the reactant, co-solvent and template. The as-prepared UCNPs were introduced into Caenorhabditis elegans (C. elegans) to achieve successful in vivo imaging. We found that longer incubation time, higher UCNP concentration and smaller UCNP size can make the in vivo fluorescence of C. elegans much brighter and more continuous along their body. The worms have no apparent selectivity on ingestion of the UCNPs capped with different capping ligands while having similar size and shape. The next generation of worms did not show fluorescence under excitation. In addition, low toxicity of the nanoparticles was demonstrated by investigating the survival rates of the worms in the presence of the UCNPs. Our work demonstrates the potential application of the UCNPs in studying the biological behavior of organisms, and lays the foundation for further development of the UCNPs in the detection and diagnosis of diseases.