Economic, policy, and resource factors within the regional integration of the Yangtze River Delta are crucial pathways for promoting the transformation of scientific and technological achievements in higher education. This study examines the multifactorial synergistic effects behind the differences in scientific and technological achievements transformation in the Yangtze River Delta from the space-time dimension, offering important insights for practical applications. Drawing on interface theory, this study constructs an analytical framework of economic integration-policy integration-innovation resource integration and employs dynamic QCA to analyze provincial panel data from 2013 to 2022. The study explores the configurational effects of economic integration, policy integration, and innovation resource integration on the transformation levels of scientific and technological achievements in the Yangtze River Delta. By combining between-group and within-group analyses, the study investigates the spatial distribution differences in provincial coverage. The findings reveal that no univariate factor is necessary for high levels of scientific and technological achievement transformation. Three distinct pathways were identified in this study, which are the regional economic development-innovation resource integration model, economic integration-research collaboration model, and regional economic development-innovation resource integration model. In the temporal dimension, apart from a collective decline in pathway consistency in 2016 due to economic structural adjustments and reforms in research and development (R&D) funding management, there were fluctuations in consistency from 2019 to 2022, likely driven by COVID-19. In the spatial dimension, two configurations showed significant regional differences in provincial coverage distribution.