Abstract: The science and technology (S&T) transfer is a critical link in the progression of technological innovation from fundamental research to market application. Establishing an effective performance evaluation system for S&T achievement transformation holds significant guiding importance for the technological innovation endeavors and overall development of the tobacco industry. Traditional Data Envelopment Analysis (DEA) models predominantly focus on outcomes, treating the transformation process as a “black box”. Consequently, they are unable to quantify the efficiency of individual stages within the S&T achievement transformation process or elucidate the pathways through which stage-specific transformation efficiency impacts overall transformation performance. To address this limitation, this paper proposes an outcome nesting mechanism characterized by distinct stages. Utilizing a three-stage Data Envelopment Analysis (DEA) evaluation model, it constructs a performance evaluation system for scientific and technological achievements transformation. This system evaluates the efficiency at each stage of the transformation process as well as the overall transformation efficiency. By selecting the GDP Index, Purchasing Managers’ Index (PMI), and Innovation Index (CII), the paper analyzes the impact of the macro-environment, industry environment, and innovation environment, respectively, on the performance efficiency of scientific and technological achievements transformation. The framework enables the evaluation of both stage-specific efficiencies and the overall efficiency of S&T achievement transformation activities. Taking industrial enterprises within tobacco industry as a case study, the analysis encompasses 8,910 valid S&T achievement projects recorded by 19 tobacco industrial enterprises between 2011 and 2021. We have the following main findings. The efficiency of individual stages within tobacco industry’s S&T achievement transformation activities exhibits significant differentiation. The different stages of S&T have same bottleneck, i.e., the management inefficiency. The outcome nesting mechanism plays a crucial connecting role in the transformation activities, with the R&D transformation stage demonstrating a compensation effect for efficiency losses occurring in the fundamental research stage. Environmental factors exert differential impacts on S&T achievement transformation activities. To advance the S&T achievement transformation process in China, managers should implement lean human-oriented management systems, enhance the nested transmission efficiency across all stages, and concurrently adopt context-adapted strategies for S&T achievement transformation based on environmental variations.