In the realm of numerical algorithms for investigating interactions between multiphase fluids and structure, the accurate computation of moving contact lines (MCLs) dynamics and the substantial computational resource demands bring challenges in three-dimensional simulations. In this study, an improved diffuse interface-immersed boundary method is proposed to efficiently investigate three-dimensional multiphase fluids–structure interactions. The present work commences with the development of the explicit correction scheme and the simplified Dirac function coefficient, designed to efficiently implement the immersed boundary technique. To validate the effectiveness and accuracy of the proposed method, the simulations of water entry and exit for a half-buoyant sphere are carried out, which conclusively demonstrate that the proposed method offers significant advantages in terms of both efficiency and accuracy, faithfully capturing the dynamic response of solid structures and the substantial deformation of free surfaces at the three-dimensional scale. Additionally, a comparative analysis of the results obtained using the proposed method for the free water exit of a hollow sphere against previous experimental data is conducted, highlighting the promising potential of the proposed method for applications.