High-tech industrial agglomeration enhances the technological level and value of regional industries. It is considered to be a new and effective way to drive China’s regional innovation and development at present. Numerous studies indicate that high-tech industrial agglomeration contributes positively to regional innovation, but the current academic discussion on this issue has not yet reached a unified opinion. In various research contexts, it has also been pointed out that there may be a negative correlation or non-linear relationship between the two. This contradictory relationship makes it difficult to generalize the current research findings to realistic application scenarios. Therefore, to clarify the relationship between the two scientifically, this study employs meta-analysis, reanalyzing 833 effect values derived from 69 independent research samples based on Chinese data. The findings reveal a moderately positive correlation (r = 0.204) between the agglomeration of high-tech industries and regional innovation in China. In particular, high-tech industrial agglomeration significantly contributes to regional innovation under the paths of diversified agglomeration and competitive agglomeration. We further found that sampling region, measurement approach, measurement perspective, research methodology, and year of publication all exhibit significant moderating effects on the relationship between the two variables. Based on meta-analysis, this study not only scientifically responds to the controversy of the relationship between high-tech industrial agglomeration and regional innovation but also further reveals the inner conduction mechanism between the two. It is of great significance in exploring future studies in related fields.