The method of obtaining and characterizing heterogeneous formation parameters is an important basis for the reconstruction of shallow geological bodies. Geological modeling based on heterogeneous formation is intended to characterize the apparent parameters and physical and mechanical parameters of the soil with stochastic uncertainties and fuzzy uncertainties. The Weibull distribution is used to describe the local stratum information， and the Diamond-Square fractal interpolation algorithm， combined with calculation of the fractal dimension of the heterogeneous formation by the differential box-counting， is applied to calculate the overall stratum parameters. The PFC3D numerical simulation software， combined with data sampling by the Markov chain Monte Carlo method， is used to model the rock particles and soil particles in the heterogeneous formation. The simulation results of the heterogeneous formation indicate that its failure process and stress-strain curve are much more complicated than those of the homogeneous formation since the content and distribution characteristics of large rock particles have a significant impact on the mechanical properties of the soil. The modeling method in this paper is helpful to the study on heterogeneous formation parameter characterization.