An aqueous negative contrast agent for CT imaging of the gastrointestinal tract and the preparation method thereof. The agent is used in biological and pharmaceutical field. Its components and the weight percent are: hydrogel matrix 0.01-1%, micro-/nano-particles of the materials with low densities 5-50%, stabilization agents 0.1-5%, the rest is deionized water. The preparation method is: stabilization agents are added into the hydrogel matrix made of natural or synthetic hydrophilic polymers, then micro-/nano-particles of the materials with low CT densities are added or prepared, and uniformly dispersed in the hydrogel matrix. The CT density of the resulted aqueous negative contrast agent for CT imaging of the gastrointestinal tract is −30 HU to −500 HU. It can decrease the CT density inside the intestine lumen to lower than −30 HU. The intestine wall can be depicted clearly and the CT signals intensities inside lumen are uniform. It is feasible for 3D images processing such as virtual endoscopy reconstruction with the negative contrast agent. The agent is safe, stable and nontoxic. It will not lead to diarrhea after administration. It is of great significance for the improved sensitivity and specificity of CT diagnosis for the diseases on the intestinal wall and lumen.