The traditional energy phase-out and new energy substitution are critical to achieving the dual-carbon goal. Effectively coordinating these processes is essential for ensuring China’s energy security and achieving long-term carbon reduction. First, a Multi-Level Perspective (MLP) analysis framework is developed to examine the process of the traditional energy phase-out and new energy substitution under the dual-carbon goal, focusing on the misalignment mechanisms and their types. Second, an indicator system for evaluating misalignment risks is established, incorporating four key dimensions: new energy substitution capacity, new energy substitution level, traditional energy phase-out level, and carbon emission reduction achievement. Furthermore, a time-series cobweb grey target model is developed to evaluate and forecast misalignment risks during China’s 14th and 15th Five-Year Plan periods, and risk identification criteria are proposed. Empirical results confirm the effectiveness of the time-series cobweb grey target model.