The rectangular channel with small-scale vortex generators of different heights was numerically simulated.The value of Reynolds number was from 4000 to 10000.The result showed that the characteristics of convective heat transfer and pressure drop changed because of the difference in heights of small-scale vortex generators.The mechanism of longitudinal vortices and spanwise vortices produced by small-scale vortex generators and their effects on heat transfer enhancement were analyzed.Meantime，the influence of vortices on the pressure in the channel was analyzed.The heat transfer and drag characteristics of small-scale vortex generators were evaluated with a comprehensive criterion that considered both convective heat transfer and flow drag.