Abstract: A time splitting technique is common to many free surface ocean models. The different truncation errors in the equations of the internal and external modes require a numerical adjustment to make sure that algorithms correctly satisfy continuity equations and conserve tracers quantities. The princeton ocean model (POM) has applied a simple method of adjusting the vertical mean of internal velocities to external velocities at each internal time step. However, due to the Asselin time filter method adopted to prevent the numerical instability, the method of velocity adjustment used in POM can no longer guarantee the satisfaction of the continuity equation in the internal mode, though a special treatment is used to relate the surface elevation of the internal mode with that of the external mode. The error is proved to be a second-order term of the coefficient in the Asselin filter. One influence of this error in the numerical model is the failure of the kinetic boundary condition at the sea floor. By a regional experiment and a quasi-global experiment, the magnitudes of this error are evaluated, and several sensitivity tests of this error are performed. The characteristic of this error is analyzed and two alternative algorithms are suggested to reduce the error.