Abstract: With the construction of high dam reservoirs and the appearance of high performance computers, increasingly more 3D models are used in the simulations of stratified flows in reservoirs. Influence of the vertical coordinate system on the accuracy in the simulations of small scale regions is essential to 3D modeling, but there are few previous studies on it. Based on the results of a stratified flow experiment, this study focuses on evaluation of the effects of the most commonly used Cartesian z coordinate system and the σ coordinate system on the accuracy in flow and temperature simulations. It is concluded that both systems are applicable but with different accuracy and the σ coordinate is better. Static instability and extra vortices caused by bottom step in the z coordinate exaggerate vertical diffusivity and lead to weaker velocity and vertical temperature stratification than those in the σ coordinate. Distribution of horizontal velocity shows small scale circulations near the bottom that are caused by a spurious water falling process produced numerically in the z coordinate modeling. The isothermals also show a stair-stepping trend in the z coordinate system.