Based on Resource-based theory and Internal Control (IC) theory, this study elucidates the impacts of corporate digital transformation on total factor productivity, and IC effectiveness, as well as the mechanism among digital transformation, IC and total factor productivity. The results show that digital transformation promotes total factor productivity and IC effectiveness. And effective IC has a significant mediating effect for the impact of digital transformation on total factor productivity. Heterogeneity discussion shows that compared with high-tech enterprises, in non-high-tech ones, digital transformation increases total factor productivity, and more significantly enhances IC effectiveness, presenting a mechanism that digital transformation facilitates IC, and increases total factor productivity. For non-high-tech enterprises, with higher heterogeneity of executive education backgrounds, digital transformation promotes IC effectiveness and total factor productivity, showing the transmission effect among digital transformation, IC and total factor productivity. Finally, it is suggested that the regulatory authorities advance digital infrastructure construction, to reinforce IC and risk prevention, thereby increase total factor productivity. And enterprises grasp the opportunity of digital economy development, promote the mechanism that digital transformation facilitates IC effectiveness, and increases total factor productivity. Non-high-tech ones motivate digital elements’ governance efficacy, optimize executive structure, coordinately promote digital strategy, and help the national economy acquire high-quality development. The study provides enlightenments to achieve high-quality development.