Stratigraphic uncertainty is widely present in nature, but it has not been well considered in the stability analysis of unsaturated soil slopes in the past. In this study, the stability of the unsaturated soil slope is evaluated based on borehole data considering stratigraphic uncertainty. Firstly, an enhanced coupled Markov chain model is used to simulate stratigraphic uncertainty. Then, a finite element algorithm for automatically calculating the safety factor (FS) and the average groundwater table (AGT) of the unsaturated soil slope is developed. At last, a hypothetical slope located in the stratum from Perth, West Australia is analyzed using the proposed algorithm under different borehole schemes. The results show that with the increase in the borehole number, the statistics of FS and AGT will not monotonically increase or decrease. But the trend is that the mean values of FS and AGT gradually approach and eventually converge to the real values, and the standard deviations of FS and AGT decrease. There is a linear relationship between the standard deviation of FS (or AGT) and the average information entropy. The FS and AGT are negatively correlated considering stratigraphic uncertainty.