The evaluation of marine function zoning (hereinafter referred to as MFZ) is an important part of MFZ. This paper studies the principles of MFZ evaluation and the evaluation procedures. It is proposed that three main aspects, including the evaluation of MFZ implementation situation, the evaluation of the performance effects and the evaluation of the changes of dependent conditions, are the top priorities in establishing an evaluation indicator system framework. The evaluation of MFZ implementation situation includes assessing the general situation of MFZ and the degree of implementation and public participation. The evaluation of the performance effects involves the assessments of the achievements and the existing problems in the rectification and standardization of utilizing the sea areas, protecting marine resources and environment, and promoting marine economic development. The evaluation of the changes of dependent conditions includes the assessments and measurements of the changes in the social and economic conditions, the use demands of marine industries, marine resource conditions and marine environmental conditions. This paper provides the means of integrating quantitative and qualitative approaches into the scientific and systematic evaluation on MFZ. The evaluation results can determine whether MFZ needs to be altered or not. The results also provide an important reference basis for determining whether a slight or great alteration is justified. To illustrate the utility of the MFZ evaluation indicator system, an evaluation example is given. Further studies are needed to make the evaluation of MFZ more scientific, reasonable, fair and effective.