Marine pipelines are widely used in offshore engineering and are highly vulnerable to accidental damage caused by underwater structures such as ship anchors and deep-sea submersibles, especially in the dark and unpredictable marine environment. Research on configuration monitoring of marine pipelines is essential to ensure their operational safety. This paper develops a displacement field inversion model for marine pipelines under the influence of three-dimensional background ocean currents, based on the inverse finite element method. The model consists of an input parameter module, a coordinate conversion module, and a displacement reconstruction function module. It takes into account key characteristics such as large curvature, three-dimensional coupling with large displacements, and local flipping behavior. The proposed approach addresses the technical challenges associated with low-order deformation modes and irregular displacement patterns. The impact of the number and layout of monitoring points on the accuracy of displacement field inversion is studied. The results show that the layout with a monitoring point spacing of 100 m and an angle of 30° can meet the engineering accuracy requirements. The findings of this paper can provide valuable insights and methods for the design of marine pipeline health monitoring systems.