Ocean Acoustic Tomography is a well-known technique for acoustic remote sensing of the temperature, water velocity, and current today. This technique makes it possible to probe the ocean where is large scale or difficult to deploy instruments. In this study, we build an inverse method to estimate the ocean current from the travel time perturbation of eigenrays which was calculated by NTU-RAY. NTU-RAY is a numerical model which is included in NTU-GBM (Gaussian Beams Model). The purpose of this study is to estimate the feasibility of an experiment in the north-eastern sea of Taiwan in the future. The method is tested first in an idealized environment, such as Pekeris waveguide, and then applies to the real ocean scenario. Results show that the inverse method works well generally but with limitations. (This work is sponsored by National Science Council of Taiwan under project “Physical Oceanography and Acoustic Applications at the Marine Observatory in the Northeastern Taiwan (MONET) coordination project and subproject 1: Study of Underwater Acoustic Signature Extraction and its Data Base Automation” No. NSC 101-2221-E-002-028-MY2).