Green Total Factor Productivity (GTFP) is a crucial indicator for measuring the quality and sustainability of economic growth. Its enhancement relies not only on technological progress and improved resource allocation efficiency, but also requires synergistic support from policy systems. China has implemented a series of pilot policies aimed at improving urban GTFP. However, a single pilot policy often fails to fully achieve the desired outcomes, whereas the coordinated implementation of multiple pilot policies can more systematically promote urban GTFP growth. This study focuses on the perspective of the dual-pilot policy of low-carbon city and smart city. Theoretically, it constructs an analytical framework for how dual-pilot policy affects GTFP. Empirically, based on panel data of 284 prefecture-level cities in China from 2003 to 2022, it employs a super-efficiency SBM model incorporating undesirable outputs to measure urban GTFP and systematically demonstrates the specific effects of dual-pilot policy on GTFP enhancement using a multi-period difference-in-differences model. The main findings are as follows: (1) The dual-pilot policy effectively improves urban GTFP; (2) The GTFP enhancement effect of dual-pilot policy exceed that of individual low-carbon city or smart city pilot policy, with cities transitioning from single to dual-pilot status showing significant GTFP improvement, particularly when both policies are implemented simultaneously; (3) The dual-pilot policy fails to significantly boost GTFP in samples with superior environmental baselines, low entrepreneurial activity, or short policy implementation periods, whereas it demonstrates the strongest GTFP promotion effects in cities with moderate environmental baselines, highest entrepreneurial vitality, and longest policy implementation; (4) The dual-pilot policy positively influences urban GTFP primarily by reducing energy consumption per unit GDP, accelerating urban digital transformation, and facilitating industrial upgrading. The marginal contributions of this study are threefold: First, it systematically investigates whether the coordinated implementation of dual-pilot policy—“low-carbon city pilot” and “smart city pilot”—effectively enhances urban GTFP, thereby enriching the theoretical literature in this field. Second, it constructs a framework to systematically demonstrate the synergistic and complementary mechanisms through which dual-pilot policy promotes urban GTFP, unveiling the “black box” of intrinsic interactions among multiple policies. Third, it explores heterogeneous patterns in the effects of dual-pilot policy, revealing that policy effectiveness is significantly correlated with urban ecological environmental baselines, entrepreneurial activity levels, and policy implementation durations, while also evaluating three potential indirect effects: energy consumption reduction, digital transformation acceleration, and industrial structure upgrading. The conclusions of this study provide theoretical and practical insights for China’s exploration of green development pathways, the improvement of urban GTFP, the consolidation of early achievements from low-carbon city and smart city pilot policies, and the full realization of the potential synergies from the coordinated use of multiple policy instruments.