Manufacturing agglomeration and energy conservation and emission reduction serve as important levers and target functions for high-quality development in China, significantly influenced by the level of digital innovation and the uncertainty of economic policy. Based on the dual role of digital innovation and the hierarchical moderating effect of economic policy uncertainty, this study utilizes panel data from Chinese provinces and employs a spatial Durbin model combined with multi-scenario analysis to conduct an in-depth exploration of the impact of manufacturing agglomeration on carbon emission performance. The study finds an 'N'-shaped curve relationship between manufacturing agglomeration and carbon emission performance, indicating a win-win situation for economic growth and carbon emission performance once manufacturing agglomeration reaches a certain threshold. Digital innovation plays a dual role: as an outcome, there is an inverted 'U'-shaped curve relationship between digital innovation and carbon emission performance; as a process, it positively moderates the relationship between manufacturing agglomeration and carbon emission performance, with a stronger positive moderating effect under higher economic policy uncertainty scenarios. Further analysis shows that, under different scenario combinations, manufacturing agglomeration exhibits differentiated characteristics affecting carbon emission performance. This research provides valuable policy insights for promoting high-quality development of regional manufacturing in China, achieving dual carbon targets, and facilitating Chinese-style modernization.