Marine pipelines are widely used in marine engineering equipment, and are highly susceptible to accidental damage from underwater structures such as ship anchors and deep submersibles in the dark and unknown ocean. Conducting the marine pipelines configuration monitoring research can effectively ensure the safety of pipelines. This paper develops a displacement field inversion model for marine pipelines under the action of three-dimensional background ocean currents based on the inverse finite element method. It includes input parameter modules, coordinate conversion modules and displacement reconstruction function modules. The characteristics of large curvature, three-dimensional coupling large displacement, and local flipping are considered. It solves the technical problems caused by the low modes and irregular displacement. The number and layout of monitoring points on the accuracy of displacement field inversion are studied. The arrangement of measuring points with a spacing of 100m and 30°can meet the engineering accuracy requirements. The research results can provide certain ideas and methods for the design of marine pipeline health monitoring systems.