A diffuse optical tomography system with chaotic laser is proposed for the three-dimensional optical phantom. The high signal-to-noise ratio is beneficial to improve the spatial resolution of diffuse optical tomography. It is essential to drive the chaotic laser as the incident light into the optical phantom. The transmitted light emitted from phantom as the detection light and a part of the incident light as the reference light to carry out cross-correlation analysis. The high-density source-detector configuration in parallel plate structure is designed for detecting targets in the phantom. The propagation of chaotic laser in the phantom is studied theoretically and experimentally based on the diffusion equation. Image reconstruction is achieved by the cross-correlation analysis of chaotic laser and the Newton-Raphson nonlinear algorithm. The performance of the proposed system has been assessed by reconstruction localization accuracy and contrast-noise-ratio. The results show that the spatial resolution of the proposed system can reach 1.5 mm and the localization error is less than 1 mm.