This study provides a comprehensive analysis of the dynamic evolution of complexity and synchrony between the carbon market and the new energy market from 2019 to 2023, employing multiscale sample entropy and cross‐sample entropy methods. The study shows that, both in the long term and short term, the complexity of the new energy market consistently exceeds that of the carbon market. Additionally, the carbon and new energy markets exhibit higher synchronization on smaller scales. As the time scale increases, interactions between the carbon and new energy markets become more complex and diverse. According to these findings, it is recommended that policymakers improve the transparency of the new energy market, optimize the operational mechanisms of the carbon market, and ensure that carbon reduction strategies and new energy policies are mutually coordinated. This holds significant importance for both carbon reduction targets and the development of new energy.