Abstract: Internal multiples are commonly present in seismic data due to variations in velocity or density of subsurface media. They can reduce the signal-to-noise ratio of seismic data and degrade the quality of the image. With the development of seismic exploration into deep and ultradeep events, especially those from complex targets in the western region of China, the internal multiple eliminations become increasingly challenging. Currently, three-dimensional (3D) seismic data are primarily used for oil and gas target recognition and drilling. Effectively eliminating internal multiples in 3D seismic data of complex structures and mitigating their adverse effects is crucial for enhancing the success rate of drilling. In this study, we propose an internal multiples prediction algorithm for 3D seismic data in complex structures using the Marchenko autofocusing theory. This method can predict the accurate internal multiples of time difference without an accurate velocity model and the implementation process mainly consists of several steps. Firstly, simulating direct waves with a 3D macroscopic velocity model. Secondly, using direct waves and 3D full seismic acquisition records to obtain the upgoing and downgoing Green’s functions between the virtual source point and surface. Thirdly, constructing internal multiples of the relevant layers by upgoing and downgoing Green’s functions. Finally, utilizing the adaptive matching subtraction method to remove predicted internal multiples from the original data to obtain seismic records without multiples. Compared with the two-dimensional (2D) Marchenko algorithm, the performance of the 3D Marchenko algorithm for internal multiple predictions has been significantly enhanced, resulting in higher computational accuracy. Numerical simulation test results indicate that our proposed method can effectively eliminate internal multiples in 3D seismic data, thereby exhibiting important theoretical and industrial application value.