The green building certification system of Taiwan, EEWH (Ecology, Energy Saving, Waste Reduction and Health), has been in operation for more than 20 years (since 1999). In order to understand the relationship between green building certification and the construction costs of residential buildings, this study obtained 37 green building-certified residential cases and 36 general residential cases available from public information and conducted a comparative analysis. The results of this study showed that the average construction cost of a green building certification residential building was only 1.58% higher than a general residential building, indicating that green building certification does not require a large increase in costs. However, for residential buildings, achieving a high-grade (gold-grade or diamond-grade) green building certification means an increase of 6.7% to 9.3% in construction costs. This shows that the pursuit of higher levels of green building certification does require higher construction costs. In addition, the results of this study can not only provide important references for the government in making green building policies, but also offer a practical strategy for developers for decision-making.