Abstract: To enhance risk management capabilities for shield tunnel engineering in soft soil regions under limited exploration data, this study proposes an innovative methodology integrating an improved three-dimensional coupled Markov chain(ICMC3D)with Unity 3D roaming technology. Based on the collected borehole data, we optimized non-coaxial information and employed a back analysis method to estimate the transition probability matrix. A 3D stratigraphic model with a 199×139×60 grid was constructed, and the most likely stratigraphic distribution was obtained through 100 simulations. The uncertainty of the stratigraphy was quantified using information entropy theory. Within the Unity platform, curved tunnel alignment was generated with Bézier curves, excavation processes were dynamically simulated by Boolean difference operations, and transparent strata-tunnel integrated 3D roaming was achieved. Results demonstrate that the enhanced ICMC3D model effectively characterizes stratigraphic anisotropy, identifying soil boundaries and weak interlayers as high-risk zones. The developed 3D tunnel roaming function enables visualization of geological cross-sections and dynamic display of the excavation progress through strata. It integrates the quantification of geological uncertainty with real-time visualization, providing decision support for tunnel design and construction, thereby reducing tunnelling risks.