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The geo-structures embedded in the multiple variable strata could be significantly affected by the geological uncertainty. The quantitative evaluation of geological uncertainty and its influence on the structural safety of embedded tunnels are seldom studied in the past. This paper aims to analyse the effect of geological uncertainty on the structural performance of tunnel using the proposed stochastic geological modelling framework. The geological uncertainty is characterized using an improved coupled Markov chain model based on sparse limited boreholes. A mapping approach is presented to solve the mesh asymmetry problem between the simulated strata and the numerical tunnel model. The tunnel structural performance analysis is then conducted based on the combined model considering the geological uncertainty and tunnel structure. A geological uncertainty index (GUI) is proposed to quantitatively evaluate the level of uncertainty of each borehole and the whole site. The effect of the borehole layout scheme on uncertainty evaluation of factor of safety of tunnel structure is investigated by a large number of stratigraphic realizations. Boreholes collected from Norway with relatively more considerable variability and from Shanghai with relatively more minor variability are adopted as case studies to illustrate the proposed probabilistic analysis framework. The results show that the boreholes with larger GUI values and closer to tunnel locations have a greater weight to affect the embedded tunnel structural performance in uncertain geological strata. [ABSTRACT FROM AUTHOR]