The increase of ships crossing encounter in the intersection water of bidirectional navigation Y-fairway (YF) seriously decreases the port service level. So it is necessary to study the ship traffic rules in YF intersection water to improve this phenomenon. This paper first analyzes the ship navigation characteristics in YF intersection water. Then a simulation model for ship sailing operation system of YF is built to study the influence of different traffic rules on port service level. Traffic rules separately are First Come First Serve (FCFS), Larger Ship Priority (LSP) and Ship Leaving Port Priority (SLPP). Finally, a case study is introduced to analyze the influence of each rule on port service level. The results show that traffic rules have little effect on port service level for smaller scale ports. But LSP maintains higher port service level with the increase of port scale, while SLPP reveals obvious advantage if port scale continues increasing. And the advantage of SLPP is more and more obvious with the increase of port scale.