Abstract: Based on Navier-Stokes equation, the model equation has been deduced through algebraic coordinate transformation, then under this coordinate, the three-dimensional flow field is split into many layers along its depth and the model equation in each layer is integrated. As to numerical solving method, split step characteristic difference approximation and Galerkin lumping coefficient matrix definite element method are utilized. In a practical application,three-dimensional calculation to the tide current in the Lianzhou Bay, Zhuang Autonomous Region of Guangxi is done.