Constraining ecological footprint (EF) has become an important policy priority to reach the carbon neutrality goal and deal with environmental issues, as it represents the socio-economic pressures on the environment. Current studies on the impact of collaborative innovation (CI) on EF is insufficient, although CI contributes to scientific productivity which benefits the technological progress in clean technology. In addition, seen from different perspectives, whether CI is effective in reducing EF has remain controversial. To further clarify this issue, this paper took Guangdong-Hong Kong-Macao Greater Bay Area (GBA) of China as a case, calculated EF between annual periods of 2008-2018 at the municipal level, measured CI from four dimensions and applied threshold regression models to compare the impact of CI on EF across different economic intervals. The findings showed that: the EF of GBA displayed an overall upward trend with prominent spatial heterogeneity during the study period. The impact of CI on EF presented a double-threshold effect when examined with different indicators. Among which, the flow of scientific personnel and capital boosted EF, which intensified with economic development; while collaboration in technology exerted significant inhibitory effects on EF, and the influence of inter-city knowledge collaboration was limited. This might inspire policymakers to adopt sustainable strategies depending on the type of CI and the economic status of the city to constrain the growth of EF, thus minimizing impacts of human activities on the environment.