Present paper aims to develop a three dimensional frequency domain panel method to investigate the hydrodynamic performance of two parallel ships in close proximity with forward speed. As for present method, the Rankine source is adopted; meanwhile, the linearized free surface condition based on a double body or uniform basis flow, which can be shorten as “DB” or “Neumann–Kelvin (NK)”, is derived. As for the radiation condition at infinity, a simple combined evaluation method (SCM) is proposed, which is validated through comparison with numerical results from combined boundary-integral equation method (CM, the whole fluid domain is decomposed into the far-field and the near-field, and the Rankine source & 3DTP is used for the far-field and near-field domain, respectively, to satisfy the radiation condition exactly) and experimental results. Furthermore, present method is applied to evaluate hydrodynamic performance of two parallel ship models. Meanwhile, numerical solutions evaluated by “NK” method and “LFS-DB” method were also given for comparison. Results for present various numerical method agree with those of model experiments. Generally speaking, results from“DB” method show better agreement.