Abstract Better computational stability is achieved in an improved version of the National Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics (LASG)/Institute of Atmospheric Physics (IAP) Climate Ocean Model, version 2 (LICOM2, the standard version), after improvements to the implementations of the vertical mixing, mesoscale eddy parameterization, and bottom drag schemes. The large warm biases of LICOM2 in the western Pacific Ocean and eastern Indian Ocean warm pool and on the east coast of the Pacific Ocean are significantly improved. The salinity bias in the tropical Pacific Ocean related to the warm bias of the warm pool is also alleviated. The simulation of the Atlantic meridional overturning circulation is improved because of enhanced vertical mixing in the high latitudes of the North Atlantic Ocean. The new version also presents a stronger Deacon cell, and thus a more powerful Antarctic Circumpolar Current that is closer to the observation, due to weaker southward mesoscale eddy transport in the Southern Ocean.