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As the leading urban agglomeration in China, the Yangtze River Delta (YRD) is experiencing a factor-driven to innovation-driven transition. However, the dynamics of regional innovation growth are not yet fully understood. This paper combines the complex network methodology with spatial econometrics to disentangle the contributions of innovation endowments, innovation network flows, and innovation network positions to regional innovation growth, as well as their spatial spillover effects. The primary findings suggest that regional innovation growth results from the networked agglomeration economies, which is shaped by the interactions between agglomeration factors and network factors. Specifically, agglomeration factors play a fundamental role in regional innovation growth. In contrast, network factors, such as the network flows and network positions, may contribute to new path creation by promoting access to external innovation resources. Additionally, the institutional factors show multiplexity in fostering regional innovation patterns. Such findings indicate that the YRD region should shift the innovation growth pattern from competitive involution to mutually beneficial cooperation to reduce regional disparities. In this regard, the institutional capacity of organizing network flows and fostering reciprocal inter-city partnerships has become increasingly critical for promoting sustainable innovation and regional development. [ABSTRACT FROM AUTHOR]