Equal-spaced borehole drilling is commonly adopted in practice for site investigation, which ignores spatial uncertainty and might result in insufficient site characterization. Model-driven precise drilling is regarded as a potential solution. In this study, an uncertainty-driven peak-integration (UP) strategy is proposed to improve decision-making in 3D borehole planning. The UP strategy consists of stratigraphic uncertainty modelling and peak-integration method. The random field-based uncertainty modelling approach has been improved by employing stratum-informed Scales of Fluctuation and a novel site division method to capture the site-specific uncertainty distribution with sufficient interpretation. The peak-integration method is proposed to consider the uncertainty around peaks, as improvement of existing peak uncertainty-based borehole planning strategy. To provide an objective evaluation for borehole layout planning, a new index “Contribution of Borehole” (CoB) is proposed for the first time, using the Earth Mover's Distance, to quantify the net changes of stratigraphic distribution revealed by additional boreholes and offer validation for every decision-making. The feasibility and practicability of the proposed strategy are demonstrated by applying to an artificial geological model created based on real borehole data. The superiority of the proposed strategy is elucidated by comparing with equal-spaced strategy, via both CoB and conventional entropy reduction with detailed discussion.