<p>Subsurface stratigraphic configuration at a site is often challenging to characterize accurately, due to the complexity and inherent spatial variability of strata, along with the limited availability of site investigation data; thus, considerable stratigraphic uncertainty is induced. Site investigation aims to characterize and reduce this uncertainty, whereby borehole and geophysical explorations are the most widely used exploration techniques. However, borehole and geophysical data are often considered as separated information in existing studies. To this end, this paper presents a novel approach for characterizing stratigraphic uncertainty by merging borehole and geophysical data. In this approach, the probability distribution of geophysical parameter corresponding to a specified stratum can be derived based on both data collected at the same locations. Next, the probability of stratum existence can be estimated based upon geophysical data and the evaluated probability distribution of geophysical parameter. Then, potential stratigraphic realizations can be sampled systematically with the conditional random field theory, based upon borehole data and the estimated probability of stratum existence. Two illustrative examples with different stratigraphic structures are analyzed to demonstrate the effectiveness and versatility of the new approach. Further, a series of comparative analyses are performed to reveal the influences of types of site investigation data and their statistical error on site characterization quantitatively, through which the advantages of the fusion of borehole and geophysical data can be illustrated.</p>