The oceanic Meridional Overturning Circulation (MOC) in the present day is dominated by the Atlantic MOC, which transports huge amount of heat from the tropical region and Southern Hemisphere to the northern high latitudes. The variations of AMOC and associated oceanic heat transport (OHT) have significant influence on climate variability on many different timescales. However, whether MOC was similarly important in other periods of the Earth history and what determines the strength of MOC are unclear. Here we investigate these problems by using an atmosphere-ocean circulation model, with a focus on the Paleozoic. The Paleozoic has the advantages of simple continental configuration; it has only one vast ocean and most of its continents were located towards the Southern Hemisphere, making the mechanistic analysis easier. Moreover, the Paleozoic hosts two ice ages, one in the late Ordovician (~440 Ma) and another spanned the Permian and Carboniferous peaking around 290 Ma. Our simulation results show that the global MOC during the whole Paleozoic sank in the southern high latitudes and upwelled from the Northern Hemisphere. The strength of the MOC was primarily controlled by the westerly wind stress over the northern mid latitudes, which itself was controlled by the volume of continents within that region rather than by climate. That is, the Paleozoic MOC was primarily controlled by paleogeography. Further tests of the sensitivity of MOC strength to atmospheric CO₂ concentration indicate that the 440 Ma MOC strengthens with the lowering of CO₂, constituting a negative feedback to climate cooling. In contrast, the 290 Ma MOC weakens with the lowering of CO₂, acting to enhance the cooling. This opposite responses of MOC to CO₂ change in the two periods might be the reason why the Permo-Carboniferous ice age was much more severe than the Ordovician ice age, demonstrating the importance of MOC in deep-time climate.