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<h4>Objectives</h4> The improvement of the manufacturing industry’s total factor productivity depends not only on innovation factor double circulation, but also on cross-border mobility to a large extent. <h4>Methodology</h4> This paper constructs a model that demonstrates the impact of innovation factor double circulation and cross-border flow on the manufacturing industry’s total factor productivity, and it seeks to estimate this impact by using panel data from China’s manufacturing industry taken from the period 2009–2020. <h4>Findings</h4> It finds the path dependence of innovation factors significantly increased their double circulation cost, and did not significantly improve the manufacturing industry’s total factor productivity. <h4>Conclusion</h4> It finds the path dependence of innovation factors significantly increased their double circulation cost, and did not significantly improve the manufacturing industry’s total factor productivity. Cross-border flow improves the marginal efficiency of innovation factors, realizes the spatial agglomeration of high-end innovation factors and greatly promotes the double circulation of innovation factors in a way that effectively improves the manufacturing industry’s total factor productivity. <h4>Implications</h4> These conclusions have profound policy implications: cross-border flows can promote the incremental adjustment of innovation factors; fully release the development potential and toughness of the dual circulation of innovation factors; and are essentially conducive to improving the manufacturing industry’s total factor productivity.