China’s economy has shifted from high-speed development to high-quality development as the marginal benefits of the traditional growth model decline. This study explores how new quality productive forces (NQPFs) drive industrial structure upgrading via factor endowment upgrading and factor synergy, with the goal of addressing development bottlenecks. Using 2013–2024 provincial panel data, NQPFs are measured through the entropy weight-TOPSIS method (factor endowment upgrading) and a coupled coordination model (factor synergy), integrated into a comprehensive index, and analyzed via two-stage least squares (2SLS) regression. The empirical results show that China’s NQPFs are in their initial stage, with factors still in the process of accumulation and adaptation. NQPFs significantly promote industrial structure advancement and rationalization, with factor synergy outperforming factor endowment upgrading. Its promotion of advancement is universal, but its impact on rationalization is regionally heterogeneous, with inadequate transmission in underdeveloped and high-environmental-regulation provinces and ineffective dual mechanisms in manufacturing-led provinces. Notably, the driving effect of NQPFs on manufacturing upgrading is stronger than that on services. This study provides guidance for NQPF cultivation and contributes to the theory and Chinese practice of industrial structure upgrading from a dual-factor perspective.