With the quick advancement of wireless communication networks, the need for massive multiple-input-multiple-output (MIMO) to offer adequate network capacity has turned out to be apparent. As a portion of array signal processing, direction-of-arrival (DOA) estimation is of indispensable significance to acquire directional data of sources and to empower the 3D beamforming. In this paper, the performance of DOA estimation for massive MIMO systems is analyzed and compared using a low-complexity algorithm. To be exact, the 2D Fourier domain line search (FDLS) MUSIC algorithm is studied to mutually estimate elevation and azimuth angle, and arbitrary array geometry is utilized to represent massive MIMO systems. To avoid the computational burden in estimating the data covariance matrix and its eigenvalue decomposition (EVD) due to the large-scale sensors involved in massive MIMO systems, the reduced-dimension data matrix is applied on the signals received by the array. The performance is examined and contrasted with the 2D MUSIC algorithm for different types of antenna configuration. Finally, the array resolution is selected to investigate the performance of elevation and azimuth estimation. The effectiveness and advantage of the proposed technique have been proven by detailed simulations for different types of MIMO array configuration.