Due to the conductivity of seawater, inductive power transfer (IPT) system will bring serious eddy current loss when transmitting energy in seawater, which will not only reduce the system efficiency, but also affect the magnetic field distribution. Therefore, the equivalent model of loosely coupled transformer (LCT) in air is no longer applicable to seawater environment. In order to establish an accurate underwater LCT model, this paper considers the complex boundary conditions formed by the base station, seawater and spacecraft, obtains the expression of the phase angle of the induced electric field by using Maxwell's equations, and analyzes the phase angle offset and frequency relationship. Then, the eddy current loss of seawater is equivalent to the loss caused by coil eddy current resistance, and the underwater LCT model is obtained. In order to reduce the eddy current loss in seawater, this paper proposes the method of selecting compensation topology to reduce the current flowing through the coil, and analyzes the topology selection method under different gain conditions by taking two constant voltage topologies LCC-S and S-LCC as examples. Finally, the underwater IPT system experimental platform is built, and the experimental results verify the correctness of the theoretical analysis.