In Shanghai, the foundations of three super-tall buildings, 88-story Jinmao Tower, 101-story Shanghai World Financial Center (SWFC) and 121-story Shanghai Center Tower (SCT), are compensated piled raft (box) foundations with deep embedment. It is worth discussing how to make use of advantages of compensated foundation during foundation design and to estimate the wind resistance of deep embedment of foundation. Based on the analysis of the interaction of high-rise building and ground foundation, the pile raft foundations of the three buildings are analyzed using the statistical empirical formula. A considerable amount of piles can be saved after analyzing, and their bearing capacities and deformations of the foundations can still meet the design requirements. Meanwhile, the capability of optimizing design is further discussed, and the diaphragm wall is proven to be able to share a considerable amount of load. The re-analysis of the relevant cases puts forward suggestions for further improving the design theory of the deep buried pile raft foundation, which can save a lot of investment for China.