China's economy has achieved rapid development since the reform and opening up in 1978, but large amounts of resource consumption and pollutant emissions have significantly affected the ecological environment of some regions, therefore attention has been paid to the concept of green development and innovative development. Technological progress and innovation investment is an important way to improve the level of green development. The Guangdong-Hong Kong-Macao Greater Bay Area is a good case study area for examining the contribution of innovation investment to improving green development level in different periods, as this area, one of the regions with the highest degree of openness and the strongest economic vitality in China, has experienced a rapid developing process driven by labor-intensive industries and high-energy consumption industries, and has started the transformation to green development. Taking the cities in the Greater Bay Area as examples, this paper measures the intensity of innovation input and the efficiency of green economy in each city from 2000 to 2017, and discusses the changes in the ways and sizes of the impact of urban innovation input on improving the efficiency of green economy in different periods. This paper mainly comes to the following conclusions. (1) Most cities in the Greater Bay Area have achieved significant improvement in innovation input intensity from 2000 to 2017. During this period, Shenzhen was in the leading position in innovation input intensity, while Guangzhou and Hong Kong had slow growth in innovation input. (2) From 2000 to 2017, there was a big difference in the change of the efficiency of green economy among cities in the Greater Bay Area. The efficiency of green economy in cities in the stage of stable development usually increased steadily, while that in cities in the stage of rapid growth often fluctuated. (3) From 2000 to 2017, the main influencing factors of urban green economy efficiency in the Greater Bay Area gradually transitioned from scale effect to innovation effect, and the contribution of innovation input intensity to the improvement of urban green economy efficiency increased significantly. (4) With the maturity of urban development and the increase of industrial scale, the innovation effect will play a more important role in improving the efficiency of urban green economy.