This paper focuses on the layout optimization and hydrodynamic investigation of wave energy converter (WEC) array. For hydrodynamic analysis, each buoy is modeled as a truncated floating cylinder that can move with five degrees of freedom. The hydrodynamic response of such an array is analyzed by a semi-analytical method. Then, the power extraction by the array is used as the objective function for layout optimization. To improve efficiency, especially for an array with a large number of WECs, a novel hierarchical optimization method based on matrix coded genetic algorithm is proposed. Within this method, a large-scale array is firstly divided into several levels of small-scale arrays which are easy to handle, then, the genetic algorithm developed in this paper is used to optimize the small array of each level. An example of two-level optimization is given in this paper and compared with the result by conventional optimization routine. Finally, we investigate the influence of introducing other degrees of freedom, besides the heave mode, on the performance of arrays. Results show that as the constraints get weaker in non-heave directions, the effect of other degrees of freedom on the WEC array interaction factor becomes more and more obvious.