Emergy analysis can analyse the resource utilization and environmental performance of a system. The majority of the process industry systems belong to multi-product systems, but mistakes often occur when emergy analysis is carried out to a multi-product system due to misunderstanding of the emergy concept and lack of understanding of the system structure. To avoid the mistakes, multi-product systems are classified into two categories: inseparable multi-product systems and semi-independent multi-product systems, both of which are theoretically distinguished, and a systematic procedure of emergy analysis is proposed to avoid mistakes. Finally, a case study of biodiesel production is adopted to demonstrate the methods.