Based on the complexity of the stratum, the inherent spatial variability and the limited drilling information, the formation of the engineering geological body is difficult to accurately characterize, resulting in the uncertainty of the stratum, which in turn leads to the uncertainty of the prediction performance of the geotechnical engineering system. Therefore, a Markov-Monte Carlo (MCMC) stratum simulation method based on sparse drilling is proposed. This new method is applied to the case, and the uncertainty of stratum simulation is intuitively reflected by random simulation, which can be used for the layout of drilling scheme and geological modeling.