With the promotion of the dual carbon policy and the process of transforming and upgrading manufacturing, vigorously developing high-tech manufacturing with high-technology content and significant added value has become a powerful driving force to improve the development of the regional economy. In this regard, this research employs the two-stage network SBM-DEA method with undesirable outputs and multi-stage activities involved in the green production process. We examine the green technology innovation efficiency of high-tech manufacturing in the Yangtze River Delta (YRD) region from 2010 to 2020. We divide the activities of the high-tech manufacturing industry into two sub-stages, namely, the research and development (R&D) stage and the result transformation stage. The results are as follows: (1) The efficiency level of green technology innovation in Shanghai is at an outstanding level, having the most significant performance both in the R&D stage at 0.833 as well as in the result transformation stage at 1.006. (2) Anhui’s green technology innovation efficiency is mainly driven by the R&D stage. Green technology innovation efficiency in Jiangsu province depends primarily on the stage of result transformation, but there is still room for improvement in resource allocation. (3) Zhejiang needs to catch up in both the R&D stage and the result transformation stage, as well as to optimize the resource allocation of the green technology innovation process.