The design of geotechnical structures depends significantly on soil stratigraphy. The determination of geological stratigraphy is generally based on site investigations such as drilling, standard penetration tests and cone penetration tests. When the in-situ tests or boreholes are limited, the characterization of complex strata is difficult. The objective of this study is to develop an improved coupled Markov chain model (CMC) to simulate complex geological stratigraphy based only on limited in-situ data. The traditional CMC model is improved by developing a direction-dependent CMC method to address the strong variation of soil properties among boreholes. The difficulty in simulating different dip directions and prisms in a geological profile is solved by developing proper simulation direction in the modelling. The stratigraphy at a construction site in Hong Kong is characterized using the proposed method. It is found that both upwards and downwards inclined interfaces can be simulated very well. The prisms within a soil layer can be predicted. The accuracy of the method is closely related to the locations of the existing boreholes. The influence distance of a borehole is approximately 14 m.