The pile foundations of an overpass stretches into a shieldbored tunnel section on No. 9 Line of Shenzhen Metro. The tunnel section is excavated by mining method, with the primary support installed; then the shield goes through the mined tunnel section, with the segments erected. The tunnel section is designed by means of theoretical calculation and engineering analogy. Strengthened monitoring is made during tunnel construction so as to provide guidance for the tunnel construction. In the paper, the principle, concept and scope of the treatment of the pile foundations are determined, and the scheme of “temporary supporting the overpass and underpinning the pile foundations from inside the tunnel” is established. In the construction, comprehensive construction technologies, including temporary supporting of the overpass by means of steel pipes, pregrouting reinforcement of the tunnel crown made from inside the tunnel, installing strengthened primary support, cutting the piles, permanent supporting of the pile foundations by means of secondary lining, and installing third lining of strengthened segments, are used. The construction practices show that the tunneling has crossed the pile foundations successfully, the safety of the tunnel and the overpass has been guaranteed, and the influence on the environment inside and outside the tunnel has been minimized.