A multi-layer simulation program is developed to estimate the ocean current considering sea bottom geometry. The so-called $sigma$ coordinate system is introduced in vertical direction to describe sea bottom topography more accurately and effectively. Leapfrog scheme combined with Euler backward scheme is used to reduce computation error which may be possibly accumulated in time evolution by Leapfrog scheme alone. In this paper, very simple examples of rectangular basins with various bottom geometries were taken and the effect of sea bottom geometry on vertical structure of the ocean tidal current and its direction were investigated. Through comparisons between the present three dimensional calculation in which bottom topography is directly taken into consideration and the two dimensional calculation in which depth average concept is employed, it was found that magnitude of surface current and its direction could be largely affected by the sea bottom topography, particularly in shallow region with complex bottom shape.