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The complex geological condition encountered during excavation is the key challenge for tunneling projects. Therefore, tunnel design and construction require a comprehensive understanding of the subsurface geology. This study aims to reveal the effect of geological uncertainty on tunnel longitudinal deformation based on a reconstruction geological model using the improved coupled Markov chain method. The improved coupled Markov chain method makes the predicted results more suitable for the possible stratigraphic distribution by optimizing the transition probability matrix, and breaks through the limitations of non-coaxial predicted cell updating in traditional methods. A mapping method was proposed to establish a matching relationship between the irregular grids of the geological model and the numerical tunnel model. Then, a long tunnel in Shenzhen was selected as a case study to demonstrate the effectiveness of the proposed framework. The correlation coefficient was used to verify the relationship between tunnel deformation and the surrounding stratum with different tunnel cover depths. The geological uncertainty of various strata was quantitatively measured based on the proposed geological uncertainty index. The three-dimensional strata surrounding the tunnel were reconstructed based on exceedance probabilities for adverse geological conditions. Quantitative analysis was conducted on the tunnel vertical convergence during the excavation process. • A computational framework for 3D tunnel excavation had been designed by taking into account geological uncertainty. • The relationship was revealed between the weighted elastic modulus of strata and tunnel deformation. • The GUI and exceedance probability were defined to quantify the geological uncertainty. [ABSTRACT FROM AUTHOR]