The rat brain trauma model is established with Feeney's method. The rat brain tissue slices are imaged with the terahertz transmission imaging system, which shows that the rat brain traumatic region has lower transmittance than the normal region. The three-dimensional modeling of rat brain is realized by the three-dimensional reconstruction technique. The model clearly reflects the spatial distribution of the traumatic region inside the rat brain. This study suggests that the three-dimensional reconstruction technique based on terahertz multi-depth slices imaging has great potential in the precise and accurate biomedical diagnosis.