This paper deals with the performance of the modified environmental contour method (MECM) for determining long-term extreme load effect in a combined wind turbine and wave energy converter system. The wind turbine of the combined system is in the operational or parked mode depending on the wind speed. In addition, the wave energy converter in this study also experiences three modes depending on the significant wave height to reduce structural responses under extreme sea states. These features make the original environmental contour method (ECM) not applicable to the prediction of the long-term extreme of some responses. However, the MECM is suitable for analysis in such a system as it includes the effect of the changes of operational mode by considering additional environmental contours. It is found that the results of the MECM agree very well with the full long-term analysis (FLTA) which indicates that the MECM is applicable for such a system. In addition, the MECM can also be used to identify important environmental conditions to include in the reduced long-term analysis (RLTA), which is similar to FLTA but only includes selected environmental conditions that contribute to the relevant extreme responses.