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The estimation of an accurate near-surface velocity model is very challenging in foothill areas. The routine stacking velocity analysis is based on horizontal-invariant velocity and flat surface assumption, which no longer holds in the case of the rugged topography and strong lateral velocity variations because it is difficult to determine a replacement velocity and the bottom interface of the weathering layer for the subsequent static correction. To address the problem of undulant surface, we propose a double-square-root (DSR) time-distance relationship to fit the kinematic information of the reflected waves and use the new travel-time equation to calculate the velocity spectra and do normal moveout. We demonstrate the advantages of our method with complex velocity models, and the numerical examples indicate that the new DSR time-distance relationship is very attractive for stacking velocity analysis for rugged topography. Therefore, it has the potential to increase the accuracy of the pre-stack time migration result using the proposed time-distance relationship.