Addressing the global warming challenge, the carbon emissions reduction potential of green building (GB) is garnering increasing attention. However, the extent to which GB can impact the eco-economic efficiency (EE) of the construction industry remains unclear. To fill this gap, based on panel data for 30 regions of China from 2003 to 2018, in this study, a comprehensive analysis of the EE and sustainable impact of GB is conducted using a super slacks-based measure (SBM-DEA), panel vector autoregression (PVAR) and threshold models. The findings reflect that only about 10% of provinces have achieved EE effectiveness, with pure technical effectiveness being a significant driving force behind this. The average comprehensive, pure technical, and scale EE show a 62.23%, 46.42%, and 31.91% improvement potential regarding the efficiency frontier. The EE in the Eastern Region is relatively high, while the Western Region surpassed the Central Region in regards to EE in the areas of scale and pure technical efficiency. EE is significantly reduced in the current period (year) when it is subject to the positive impact of a standard deviation from the existing economic level. This impact was the strongest in period 1, then gradually disappeared until period 6, aligning with the Kuznets curve’s theoretical assumption. GB awareness negatively impacted the current period, but is expected to gradually show a positive effect after period 2. The urbanization, green building awareness, and green building coverage make a very small contribution to the EE, accounting for 8.6%, 1.6%, and 9%, respectively, with early EE and economic level identified as the primary variables affecting the current EE. The impact of GB on EE exhibits a threshold effect, with the ecological effect of GB significant only in cities with economic levels higher than 11.063. This research contributes to the existing knowledge of the eco-economic mechanism of GB and provides insights for government policies, promoting the sustainable development of the GB market.