Abstract: In the context of the digital intelligence era, the core challenge of scientific research innovation evaluation has evolved from partial improvements in metrics and methods to a structural dilemma where evaluation systems fail to operate stably and cannot be embedded in scientific research governance practices. This study proposes a new paradigm termed "Intelligent Innovation Evaluation Engineering", which reconstructs the organizational logic of evaluation activities from a systems engineering perspective. Supported by explainable artificial intelligence, grounded in open sharing as an institutional foundation, and realized through modular engineering integration, this paradigm comprises five synergistic modules: data integration and shared services, dynamic management of evaluation indicators, modeling of scientific research management processes, mapping mechanisms between indicators and processes, and intelligent tool construction. The objective is to upgrade scientific research innovation evaluation from fragmented and closed tool-based research to an integrated, open, and sustainable socio-technical system, thereby enhancing the reproducibility, interpretability, and embeddability of evaluation systems, facilitating deep integration of evaluation into the entire process of scientific research governance, and providing a systematic solution for modernization of scientific research governance in the digital intelligence era.

Key words: Research innovation evaluation, Intelligent innovation evaluation engineering, Engineering paradigm, Open data platform, Research governance