Abstract: The super-efficiency SBM model which considers undesirable outputs is used to measure the efficiency of scientific and technological innovation resources allocation in the Pearl River Delta from 2014 to 2018 and the Malmquist index is used to evaluate the dynamic changes of the efficiency for the purpose of its improvement and the coordinated development of innovation in the Guangdong-Hong Kong-Macao Greater Bay Area. The suggestions on resource integration was finally put forward. As the results show, the scientific and technological innovation resources are mainly concentrated in cities with high level of economic development such as Guangzhou, Shenzhen and Foshan; industrial pollution places restrictions on improving the efficiency of scientific and technological innovation resources allocation; and the overall efficiency of scientific and technological innovation resources allocation in the Pearl River Delta is high, with Shenzhen ranking first and Jiangmen and Zhaoqing ranking last. According to the Malmquist index decomposition, technological development is an important factor in the difference of efficiency of scientific and technological innovation resources allocation.