Earth pressure balance (EPB) culvert jacking tunnelling, combining with pipe-roof preconstruction method (PPM), offers a competent solution particularly for constructing large shallow underpass tunnels in urban environments. However, technical knowledge gaps exist regarding its applicability, primarily due to a lack of project case studies and field monitoring data. This study specifically investigates the ground deformation characteristics associated with EPB culvert jacking tunnelling, based on the world’s largest to date culvert-jacked tunnel (19.8 m wide and 6.4 m high) project utilizing PPM in soft ground in China. The study provides a detailed analysis of the deformation time-history of both the ground surface and the pipe roof. Additionally, a three-dimensional numerical simulation is conducted to explore the correlation between ground deformation and both front face and lubrication grouting pressures. The key findings include that: (1) The jacking of individual culvert segment generally causes surface settlement along the tunnel axis longitudinally, with the maximum settlement change reaching 40 mm. The tunnel’s transverse section typically exhibits a V-shaped settlement trough profile, with the greatest deformation occurring at the section centre; (2) Ground deformation varies significantly during continuous jacking operation and is influenced by both ground loss and grouting pressures; (3) The pipe roof demonstrates a vertical deformation scale significantly greater (twice as much) than that of the ground surface, underscoring the pipe roof’s sensitivity to jacking-induced disturbances, while the surface deformation is mitigated by the pipe roof; (4) The three-dimensional numerical simulation reveals that increasing face pressure is initially more effective for settlement control, the effectiveness plateaus at higher pressures, whereas increasing grouting pressure continues to yield substantial reductions in settlement. These findings contribute to the safety control of EPB culvert jacking combined with PPM for large tunnel construction.