Existing studies have not fully elucidated the evolution mechanisms of surface settlement patterns during twin-pipe jacking operations in soft soil strata, nor have they adequately addressed the limitations in predictive accuracy of conventional Peck formulations. A systematic investigation was conducted employing an integrated methodology combining three-dimensional numerical modeling, theoretical analysis, and empirical validation to characterize the morphological evolution of surface settlement troughs under coupled variations in pipe burial depth and inter-pipe spacing. Subsequently, a refined predictive framework for surface settlements was developed. The findings indicate that increasing inter-pipe spacing or reducing burial depth progressively transforms settlement trough geometries from V-shaped profiles to U-shaped and ultimately W-shaped configurations. A dimensionless shape factor K was derived through parametric sensitivity analysis, enabling quantitative classification of settlement curve morphologies. To enhance the applicability of the Peck formula in twin-pipe jacking scenarios, calibrated coefficients were introduced to adjust settlement trough width and peak settlement magnitude, thereby reducing prediction discrepancies from 70% to within 5% for V-shaped and U-shaped profiles. An additional heave compensation term was incorporated to model W-shaped settlement behaviors. Validation against field-measured data demonstrates the proposed model’s efficacy in simulating surface settlements for shallow-buried twin-pipe jacking projects. The outcomes contribute novel theoretical insights and practical methodologies for optimizing settlement control in twin-pipe jacking operations within soft soil environments.