Natural rivers are usually winding with branches and shoals, which are difficult to be simulated with rectangular grids. A 3-D current numerical model was established based on the orthogonal curvilinear coordinate system and vertical σ coordinate system. The equations were discretisized using a semi-implicit scheme. The "predictor" and "corrector" steps were applied for the horizontal momentum equations to meet the basic requirement that the depth-integrated currents obtained from the equations for 2-D and 3-D modes have identical values. And a modification of traditional method of dry/wet discriminance was proposed to determine accurately the boundary and ensure the continuity of variable boundary in the simulation. This model was verified with the data measured in a winding tidal river with branches in April, 2004. The simulated data of water levels and velocities agree well with the measured ones, and the computed results reveal well the practical flow characteristics, including the vertical secondary flow in a winding reach.