It is crucial to maintain the layer sequence information on in situ lunar soil during the lunar soil sampling. In this paper, a discrete element model for direct push sampling of the lunar weathering layer is established, and the relationship between the perturbation rate of the lunar soil layer sequence information and the sampling depth is obtained. A quantitative evaluation method of the perturbation rate of the structural information on the lunar soil layer sequence based on the Gaussian curvature is proposed by reconstructing the center-of-mass point cloud model of the marked layer lunar soil particles in MATLAB. The proposed method can accurately describe the perturbation rate of lunar soil layer sequence information and can analyze the degree of lunar soil disturbance according to the displacement of the sampling tube and mechanical parameters in real-time inversion during the sampling process. When the sampling depth is 40 mm, the minimum and maximum perturbation rates of sampling along the penetration direction of the machine are 5.261 % and 27.649 %, respectively. The perturbation rate shows a trend of first decreasing and then increasing. The method proposed in this study could effectively solve the problem that the disturbance of lunar soil bedding information was difficult to evaluate in the sampling process of lunar regolith.