The spatial distribution of Ground Control Points (GCPs) is a critical factor affecting the accuracy of UAV photogrammetry in hilly terrain. Existing studies primarily focus on the influence of GCP quantity on accuracy or discuss planar distribution uniformity in flat areas, with limited systematic analysis separating horizontal and vertical distributions as independent dimensions. This study utilizes a DJI Mavic 3E UAV to acquire aerial imagery in a typical hilly area of Mengyin County, Shandong Province, with 27 high-precision GCPs deployed. Four comparative experiments combining random/uniform distributions in both horizontal and vertical dimensions are designed to quantitatively analyze the impact of different distribution patterns on aerial triangulation and mapping accuracy. Results demonstrate that the dual-uniform distribution strategy achieves optimal accuracy, with horizontal RMSE of 0.045 m and vertical RMSE of 0.039 m, representing improvements of 32.8% and 17.0% respectively compared to the random distribution scheme. Furthermore, this paper proposes the Spatial Distribution Balance Index (SDBI), which integrates Planar Uniformity Index (PUI) and Vertical Uniformity Index (VUI) with a terrain-adaptive weighting mechanism. The VUI weight, calibrated as β=0.714 via a Sigmoid nonlinear amplification function (k=15,x0=0.15), enables the SDBI to adaptively reflect terrain sensitivity to vertical control. The enhanced SDBI shows a correlation coefficient of r=−0.93 with final accuracy, validating its effectiveness as a GCP layout optimization and evaluation tool. This research provides a quantifiable technical framework for GCP deployment in UAV photogrammetry in hilly regions.