This study investigated the mechanical effects of backfill construction in the orthogonal underpass section of a full-section complex open-cut interchange tunnel. The research was based on the small-clear-distance interchange tunnel project at the extension section of Jinzhou Avenue and Xingguang Avenue in Chongqing. A combined approach of numerical simulation and on-site in-situ test measurement was adopted to analyze the influence of different backfill materials, tunnel cross-section types, and complex construction procedures on the mechanical behavior of the underpass tunnel. The mechanical effects of backfill construction in the orthogonal underpass section were determined. The following findings are revealed: During the backfill construction process, the displacement and internal force of the underpass tunnel increase gradually, with abrupt changes occurring at the end stages of the overlaying tunnel construction and the lateral backfilling. Significant stress changes are observed at the haunches and footings of the underpass tunnel. Subsequently, replacing the interface fill with C15 concrete forms a stable composite system between the upper and lower tunnels, effectively inhibiting drastic stress fluctuations in these critical zones. The displacement and internal force of the underpass tunnel structure exhibit longitudinal maxima, extending from the intersection interface toward the adjacent section. Upon completion of construction, the peak values of displacement and internal force are transmitted from the intersection interface to the longitudinal adjacent section at y = 6 m.