Inclusion of the Prandtl number variation with stratification in a vertical mixing scheme helps to improve the simulation of the tropical Pacific using an ocean general circulation model (OGCM) significantly, by mitigating various persistent problems of the OGCM such as the warm and cold biases in the central and eastern equatorial Pacific, the too weak and deep Equatorial Undercurrent and the insufficient zonal slope of the thermocline. It also makes the distributions of temperature and zonal velocity along the equator more realistic. A similar test with a different vertical mixing scheme supports the generality of the results.