Material flow analysis (MFA) is an important method for studying material metabolisms at regional and national scales. This article generalizes the status quo of MFA research in different scales. Next, a physical Input-Output Table (PIOT) is introduced as a mean of improving the analytical frameworks and accounting methods of MFA. The PIOT forms a basis framework on which all enterprises and industrial symbiosis networks in the industrial area are assessed. Finally, details concerning the study of metabolisms in Eco-Industrial Parks (EIPs) at an industrial ecosystem-scale are presented, and a EIPs-MFA model is constructed. This article concludes (1) Compared with MFA at national and regional scales, the purpose and method of EIPs-MFA are different, the object for the former studies is the socio-economic system, while for the latter it is the production system of the enterprise; (2)The former generally takes up a top-down approach, the latter bottom-up; (3)The former often treats the studied system as a black box, while the latter use a gray box; (4)Considering the particular objections of EIPs, which puts more emphasis on the metabolism of solid waste, water, and other special material flows in the park, EIPs-MFA should select these indicators above as the vital components to account and evaluate separately; (5)Last but not least, the aim of EIPs-MFA is to discern the characteristics of material flows inside and between the enterprises, and to identify and evaluate opportunities and potentials for increasing the material use efficiency through material re-use and recycling strategies.