Paper-based composite packages, which have been widely used for beverage in modern daily life, are featured of nutrition preservation and convenience. However, it is also causing environmental problems in urban areas because of the low recycling rate. The introduction of extended producer responsibility (EPR) is helpful to improving the recycling rate of beverage paper-based composite packaging by extending the producer's environmental-protecting responsibility for the product from its production to its end-of-life treatment. To find out the optimal strategy of applying the EPR system for beverage paper-based composite packaging, this paper is conducted based on the basic framework of the EPR system, combined with the specific requirements of the EPR System Implementation Plan promulgated by China and the Implementation Plan of the EPR System for Beverage Paper-Based Composite Packaging. An evaluation index system for beverage paper-based composite packaging manufacturers is constructed to perform the EPR system, including three management-level indicators, 10 standard-level indicators and 42 programme-level indicators. A comprehensive evaluation method is introduced to help the producers to fulfill the extended producer responsibility. Results suggest that beverage paper-based composite packaging producers should first fulfill the responsibility in information disclosure, ecological design and use of recycled materials.