The Beibu Gulf is at an important geographical location and rich in gas, oil and biological resources. The observed currents showed that the current in the upper layer was opposite to that in the lower layer in boreal winter in the northern Beibu Gulf and it was northeastward in the lower layer. This northeastward current was reproduced by a 3D baroclinic model in this study. It’s found that the counter-wind deep current (referred to as ‘CWDC’ hereinafter ) strengthened from September to November but weakened from December to the following February. A closed meridional circulation in vertical direction was found in the northern Beibu Gulf, including CWDC, surface southwestward current, an upwelling, and a downwelling. The temporal variation process of the meridional circulation was similar to that of CWDC, with strength and range stronger in November and December than in other four months. Similar to the variation process of CWDC, the monsoon wind changed from weak easterly wind in September to strong northeasterly wind in November and December, and it was transformed into weak southeasterly wind in February again. The sensitive experiments showed that CWDC and the meridional circulation were controlled by the monsoon wind and were adjusted by heat flux- and tide-induced mixing, respectively. According to the momentum balance equation, it can be revealed the counter-wind deep current is a compensation current which is induced by the surface elevation gradient balanced by the Coriolis force, vertical diffusion and baroclinic pressure gradient.