Abstract: Dredging of the channel has become one of the main means of expanding urban land through dredging. Analyzing the disturbance of dredging samples is a key part of the project. Based on the particle flow 3D model, we studied the disturbance characteristics of the sample structure during the penetration and proposed a fitting rotating paraboloid to evaluate the microscopic information of sample structure disturbance. Among them: the layered fitting surface characterizes the apparent deformation of the sample, and the coefficient of the structurally fitted surface quantizes the micro-disturbing zone and the destruction zone of the sample. The test can provide a reference for evaluation of engineering geology and optimization of sampler’s design, and reduce the costs on over-conservative design and construction in actual work. The results indicate that the soil particles show an upward micro-uplift and an inverted U-shaped bedding. The degree of disturbance of different bedding is different, and the degree of disturbance of different parts of the same bedding is different. The apparent deformation of the bedding can be fitted by a rotating paraboloid formula. The distribution law of the feature inflection points of each layer can also be fitted by the paraboloid of rotation paraboloid; the area outside the surface is a strong disturbance zone, and the area inside the surface is a micro-disturbance zone. The volume integral ratio of these two regions can be used as the evaluation of the originality of the sample.