The neural circuit of the central nervous system (CNS) primarily determines brain functions and, as a consequence, controls animal behavior. This paper describes an X-ray microtomographic analysis of the Drosophila larvae CNS, visualizing the neural network embedded in the three-dimensional structure of the nerve tissue. In fluorescence confocal microscopy, absorbance at emission or excitation wavelengths interferes with the fluorescence detection. In contrast, transparency of the nerve tissue to hard X-rays enables tomographic analysis of the intact CNS without sectioning. Yet the nerve tissue is composed of light elements that give little contrast in a hard X-ray transmission image. The contrast was enhanced by staining neuropils in the CNS with metal elements. The obtained structure revealed the internal architecture of the CNS. This metal-staining microtomographic analysis can be applied to any nerve tissues, thereby shedding light on the underlying structural basis of neural functions.