In the light of Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM), the internal structure of Markuelia hunanensis is revealed. In one example, vitrification and peeling show the annuli hidden under the chorion. Sectioning and 3-D reconstruction display an intact digestive tract from the inverted introvert to the terminal anus. The inverted introvert forms a rugby cavum. The following digestive tract is rope-like coiling, parallel to the body axis, about 650 μm in length, and uniform in diameter (~80 μm). An exquisitely preserved pipe-like structure is hidden in the middle of the rope-like structure, diameter 20–40 μm, with a length of ~120 μm. We interpret this pipe-like structure as the possible epidermis of the gut and its surroundings as the possible residue of musculature, similar to that in Priapulans. The two symmetrical rod-shape structures connecting the body wall and digestive tract are interpreted as the possible retractor muscles. After comparing the well preserved Left-form and Right-form Body of Markuelia, we suggest that they may represent a dimorphism. Counted directly, one sample of Markuelia hunanensis possesses 62 annulations and the other 68.