At present, the metro station constructions in dense urban areas face significant challenges during the rapid urban metro network expansion. The repeating disturbances to city traffic, commerce, and residents' daily life induced by conventional open-cut metro station constructions can no longer be accepted in dense urban areas. To solve these problems, some underground excavation methods, such as enlarging shield tunnels, shallow tunnelling method and pipe-roof mining method, have been attempted, but it is difficult for them to be adapted to the strict limitation of urban space in soft ground. In this paper, the planning, construction, challenges, and relevant key techniques of an innovative type of metro station – open-cut shafts combined with quasi-rectangular jacking boxes (SCJB) were introduced and investigated. The main conclusions are as follows: (1) For the advantages of efficient underground space utilization and little impact on traffic and environment, the SCJB method is recommended for the constructions of metro stations that need to traverse the heavy traffic roads and express-way viaducts. The flexible combinations of open-cut shafts and jacking boxes can form various layouts of underground space to adapt to various complex surrounding environment. (2) Steel-concrete composite lining was designed for jacking boxes considering the transportation convenience and bearing capacity enhancement, and the corresponding earth pressure balanced box jacking machines were developed. (3) By applying thick thixotropic slurry with small filtration loss, the jacking resistance of the large-section box culverts was effectively reduced to 4–6 kPa and the total jacking force was kept at 30,000 kN. (4) By surveying with laser guiding system and performing timely rectifications, the trajectory deviations induced by two large adjacent box jacking were controlled within ±50 mm. The horizontal convergence of east line box segments caused by the west line jacking was controlled within 1.5 mm, through strict trajectory control. The surface settlement induced by the crossing of three box jacking tunnels was effectively controlled within 15 mm. The experiences learnt from this project can provide valuable references for the planning and construction of metro stations in dense urban areas in soft ground.