In this study, hydrodynamic analysis of an oscillating water column (OWC) array in the presence of the variable bathymetry (seafloor depth) is performed by using a semi-analytical potential-flow solver. Within the framework of linear theory, the boundary-value problem associated with wave diffraction and radiation by an OWC array with variable bathymetry is formulated and the semi-analytical hydrodynamic model is developed using the matched eigenfunction expansion method. The fluid domain above variable bathymetry is mathematically discretized into multiple subdomains using the boundary approximation method. The Haskind relation and the energy flux conservation law are used to verify the semi-analytical model. The hydrodynamic performance of the OWC array in the presence of the ripple and coral reef bathymetries are investigated in further. Pronounced oscillations are observed for the curve of reflection coefficient Cr and hydrodynamic efficiency η for cases with ripple and coral reef bathymetries. Bragg resonance is identified as the triggering of the strong oscillations in Cr and η for case of ripple bathymetry. The primary frequency of Bragg resonance and the peaked value of Cr converge as the ripple number increases (i.e., Ns > 3). Particularly, for cases with coral reef bathymetry, the wave resonance modal in open-ended basins results in a significant wave amplification at the weather side of the OWC array.