The mega columns used in super-tall buildings are several meters in size; thus, a greater quantity of construction materials are required than for a general column. Considering the environmental impact, research on a green design model for super-tall buildings is necessary. This design model should minimize both CO2 emissions and cost in the mega-column construction and design phases with consideration of the member or building size. In this regard, a multi-objective green design model (MOGDM) capable of minimizing construction cost and reducing CO2 emissions is proposed in this study. The MOGDM is applied to the design of mega columns for a super-tall building and its performance is evaluated based on the average environmental impact reduction rate (AER) and the average increase-in-cost reduction rate (AICR); these indexes are developed to assess the CO2 emission and construction cost reduction capability. Under the loading scenarios considered in this study, the average AER and AICR for the MOGDM output are 6.76% and 58.02%, respectively. Thus, the evaluation results confirm that the MOGDM proposed in this study can effectively reduce CO2 emissions and cost in the design and construction phases of mega columns for super-tall buildings.