The three-turbine system is an advantageous device for tidal current energy extraction and has received widespread attention recently. In this paper a numerical model is developed to analyze the effect of tidal current directions on the performance of this three-turbine system and is validated with experimental data. This model is then used to simulate performance of the system on varying tidal current directions. It is shown that the effect of tidal current directions on the system is significant when turbines are in the same horizontal plane. The minimum relative power coefficient is only 2.19 and it is increased as the distance between turbines grows. This prominent trend is due to wake dynamic effects because the downstream turbine locates in the near wake of upstream turbines. On this basis, a new arrangement of system in which the turbines are arranged in different horizontal plane is proposed and investigated. This improved system can effectively enhance the power extraction, while effects from variations in tidal current directions are reduced. The results show that the power extraction of this improved system with optimal layout is approximately 6% higher than three isolated turbine.