The number of pit-in-pit foundation pit is increasing quickly because of the continuous utilization of underground spaces in urban areas. Based on the co-construction project of Shanghai Museum of Natural History foundation pit and Shanghai Metro Line 13 foundation pit in Shanghai, China, the deformation characteristics of pit-in-pit foundation pit are researched by field observation and centrifugal model tests. The lateral wall displacement of inner foundation pit includes global deformation caused by the outer foundation pit excavation and deflection caused by the excavation of itself. The effect of inner foundation pit excavation on the lateral wall displacement of outer foundation pit and ground-surface settlement is smaller. The two factors affecting the deformation characteristics of pit-in-pit foundation pit, the distance between inner and outer foundation pits (D) and the excavation width of inner foundation pit (W_in), are analyzed by centrifugal model tests. The result shows that the maximum lateral wall displacements of inner and outer foundation pits decrease nearly linearly with the increase of D, but increase with the increase of W_in.