High resolution imaging is an important technique for micro-nano scale objects to obtain the structural information. Micro computed tomography (micro-CT) is one of the techniques to obtain internal information without physical damage for sample. We investigate the micro-CT imaging for the Caenorhabditis elegans (C. elegans) in this paper. This is the one of the smallest animal used as a model organism, which is a biological model in the biology and medical research fields for investigating the biological system, evaluating the drugs affectivities, and so on. We used a micro-CT instrument inside an environmental scanning electron microscope (E-SEM) for obtaining small samples with water-containing condition. This set-up will be effective as a novel nanomanipulation platform to investigate three-dimensional manipulation of small biological samples, including C. elegans.