This study addresses the unclear damage mechanisms of pipe segments during long-distance pipe jacking in highly permeable rock strata. A comprehensive investigation is conducted based on the Danjiangkou river-crossing pipe jacking project, integrating both field monitoring and numerical simulations. Analysis of the full-cycle measured data on rebar stress, concrete strain, contact pressure, and mud pressure reveals that the fundamental cause of pipe segment cracking is stress redistribution induced by pipe deflection. It is further shown that the severe fluctuations in the monitoring data are due to a cyclic process of "deflection → correction → re-deflection." Through numerical simulations, the nonlinear relationship between deflection angle and the ultimate jacking force is quantified. The results show a strong correlation between the damage patterns of the pipe segments and the deflection angle. Specifically, small-angle deflections are characterized by diagonal cracks in the pipe barrel, while large-angle deflections lead to radial crushing damage at the joints. These results offer important guidance for improving construction parameters and developing effective damage control strategies in upcoming pipe jacking projects within rock strata.