[Objective] The effects of science and technology innovation on the ecological environment under geospatial constraints were studied in order to provide a theoretical basis and policy inspiration to promote ecological environmental protection. [Methods] We used survey data from 16 prefecture-level cities in Anhui Province from 2011 to 2020 with ArcGIS, Geoda, and Stata15.1 software along with an exploratory spatial data analysis method and a spatial measurement model to investigate the spatial correlation and influence effect of science and technology innovation on the ecological environment at the global and local scales. [Results] ① The ecological environmental quality and the level of science and technology innovation in Anhui Province have been steadily increasing each year. The ecological environment showed the spatial characteristics of “high in Southern Anhui Province, medium in Central Anhui Province, and low in Northern Anhui Province”. Science and technology innovation radiated most from Hefei and Wuhu City. ② The impact of science and technology innovation on the ecological environment showed a negative effect in Southern Anhui Province, and a direct positive effect and spatial spillover effect in Central and Northern Anhui Province. ③ From the perspective of Anhui Province as a whole, the degree of influence of science and technology innovation elements on the ecological environment followed the order of science and technology innovation environment ＞ science and technology innovation output ＞ science and technology innovation input, but with heterogeneous characteristics in different regions. [Conclusion] To carry out ecological environmental protection, it will be necessary to adjust measures to local conditions, determine the direction and focus of scientific and technological innovation and ecological environmental protection in various regions, highlight local advantages, and give attention to the role of radiation in the field.