Marine magnetic survey is one of the basic methods for oceanographic observation, seabed resource prospection and national defense security. Learning about the mechanism of the wave induced magnetic field, the prediction model and the methods of noise suppression are of great importance for improving the measurements accuracy. On the basis of analysing the first order Stokes wave motion equations, this paper proposes an improved model of the ocean wave induced magnetic field, together with simplified formulas for the deep and shallow water conditions. In order to verify the validity of the model, an observation was done in the South China Sea in 2015. By comparing the proposed model with the classic Weaver’s model and the test results, it is shown that the proposed modified model can make an accurate prediction which is nearly an order of magnitude higher than Weaver’s model on the ocean wave induced magnetic field. This makes the proposed model a more effective tool of noise suppression for Marine magnetic field measurement.