In the strategic background of high quality integration in the Yangtze River Delta (YRD), green technology innovation, as the combination of green development and innovation-driven national strategies, has become an important engine of green transformation and development in the region. This paper, by constructing a super-efficiency SBM-DEA model that includes undesired output, measures the efficiency of green technology innovation in core cities of the YRD from 2010 to 2017, and studies its spatio-temporal evolutionary pattern and driving forces mechanism. The results show that, (1) In terms of time series evolution, the green technology innovation efficiency in the study region shows a “W”-shape pattern. (2) In terms of spatial evolution, the green technology innovation efficiency in the southeast of the YRD is relatively stable, while changes in the central and southwestern parts are obvious, showing the characteristics of continuous agglomeration and development as a whole. (3) In terms of spatial correlation, the regional spatial relationship of green technology innovation efficiency in the YRD has gradually changed from the “polarization effect” to the “trickle down effect”. As a whole, Theil index and Gini coefficient show the characteristics of an “M” change opposite to the evolution of time series. (4) Based on the measured results of input, output and efficiency of green technology innovation in the delta region, all cities are identified into six types: high-high-high, high-high-low, high-low-low, low-high-high, low-low-high, and low-low-low This further reveals regional differences in the development path of green technology innovation in the YRD. (5) The research results of driving forces mechanism show that environmental regulation, economic development, industrial structure, opening degree to the outside world, human capital and urbanization all play significant positive roles in promoting the spatio-temporal evolution of green technology innovation efficiency in the YRD, while the innovation support has a significant negative spillover effect. (6) On the whole, the green technology innovation in the study region does have a significant “Porter Hypothesis” effect, but the “pollution paradise” effect mentioned in the literature has not been found.