In present study, a vertical line source time domain Green function is proposed and the subsequent numerical evaluation methods are described in detail. For which, Taylor expansion and Chebyshev approximation algorithms are originally extended from point source to line source for small parameters, as well as asymptotic expansions are extended for large parameters. Meanwhile, polynomials are originally proposed to replace the asymptotic expansions to improve the computational efficiency. The accuracy and stability of the proposed method are validated through several cases and good agreement can be obtained.Furthermore, a hybrid Green function method based on the vertical line source Green function and Rankine source is developed for time domain simulation of seakeeping performances of ships. With respect to the hybrid method, the flow domain is divided into inner part and outer part by an artificial control surface. The first-order Taylor Expansion Boundary Element Method (TEBEM) based on the Rankine panel distribution is applied in the inner part, while three-dimensional panel method based on the vertical line source Green function distribution is adopted in the outer part. Under this circumstance, motions of the single-ship (Slender Wigley and Blunt Wigley) and two-ship (two side-by-side ships) in head waves are numerically investigated. The numerical results agree well with the experimental data, which proved the feasibility and the accuracy of present hybrid Green function method for motion prediction of both single-ship and two-ship.