This paper modifies the BEKK-GARCH model based on the empirical results of the VAR model to analyze the dynamic volatility spillover effect between the European Union allowance (EUA) and certified emissions reduction (CER) markets during the second and third phases of the European Union Emission Trading System (EU ETS). The empirical results show that (1) an asymmetric volatility spillover effect exists between the EUA and CER markets and that the EUA market has a more significant volatility spillover effect on the CER market, and (2) the volatility spillover effect between the EUA and CER becomes weaker in phase III since the European Commission has limited the substitution of CER for EUA more strictly and the global carbon reduction requirements have become less demanding. Our study can help investors and managers of carbon market to have a more comprehensive understanding of the information and risk transmission mechanism between the EUA and CER markets, thus, providing them with a basis make investment decisions and formulate policies.