Abstract: The composite strata of coastal regions are composed of soil and rock, and the upper mucky soil has low bearing capacity. Under this condition, it is significantly important to choose suitable supporting mode to ensure the stability of deep foundation pit. However, the stepped supporting is not allowed because of the narrow construction site. The multi-layer supporting structure of deep foundation pit is proposed and numerical analysis is carried out. The finite difference software FLAC^3D is used to analyze the deflection and the pile-top horizontal and vertical displacement of retaining structure. Combined with site test and monitoring data, the deformation characteristics and support effects of the multi-layer supporting structure are investigated. Compared with the conventional supporting structure, the dosage of anchor cable (in the density) is reduced by 20% through adopting the multi-layer supporting structure, and the support system is optimized. The research results provide meaningful theoretical and practical guide for deep foundation pit in composite strata of coastal regions.