The invention provides a two-stage carbon-based catalyst regeneration tower system. The energy utilization rate in the carbon-based catalyst regeneration process is improved, and the matching propertyand flexibility of the carbon-based catalyst regeneration tower and a desulfurization and denitrification adsorption tower are enhanced. According to the system, the regeneration tower body is sequentially divided into a preparation section, a heating section, a transition section, a cooling section and an outlet section from top to bottom, wherein the heating section and the cooling section areof a tube-shell type heat exchange structure; the regeneration tower body is a tube pass; the carbon-based catalyst passes through the tube pass, and a heat exchange medium passes though the shell pass. The carbon-based catalyst enters from the tower top and reaches the bottom of the regeneration tower through the tube pass. The transition section is arranged between the heating section and the cooling section and is used for discharging SO2 gas enriched in the tower, and the discharged SO2 gas is introduced into an acid production plant.