The ground subsidence caused by rectangular soil pressure balanced pipe jacking construction in large section would damage the pavement structure layer, which has always been a difficulty and hot topic in geotechnical engineering. With the underground passage project in the Inner Mongolia University of Science and Technology as a case study, we analyzed the measured data of subgrade deformation and the applicability of Peck’s formula in predicting ground subsidence caused by rectangular pipe jacking, and also simulated the influence of pipe jacking construction in the presence of different soil depths on ground subsidence numerically. We found that, in general, measuring points in longitudinal direction on the jacking axis bulged at first, and then subsided and subsequently tended to be stable; in terms of cross section, pipe jacking affected an area within 10 meters of the axis, where the volume of settling trough occupied 90% of the total volume. When soil strata loss rate equals 0.4% and width parameter K of settling trough equals 0.4, the measured value agrees well with the results predicted by Peck’s formula. With the increase of overburden soil depth, the surface subsidence decreased gradually, and the settlement range gradually increased. The research results provide theoretical reference and application value for the construction of large cross-section soil pressure balanced rectangular pipe jacking and similar projects.