Economy-wide material flow analysis (EW-MFA) and relevant indicators have been designed to monitor material flows at the macroeconomic level and to provide indicators that could contribute to the management of resource use and output emission flows from economic, environmental, and broader sustainability perspectives. Recently, EW-MFA has been rapidly developed in theoretical research and widely used as an important tool in resource and environment management. A systematic review of the theoretical research on EW-MFA is performed in this study, and this review is expected to serve as a reference for future theoretical research on EW-MFA. First, a brief outline of the historical development of EW-MFA over the past 50 years is presented, the accounting framework and indicator systems of EW-MFA are introduced, and the pros and cons of EW-MFA indicator aggregation are discussed. Second, the state-of-the-art of EW-MFA is summarized and discussed as a key component in the accounting of EW-MFA indicators as well as the driving forces and dynamics of EW-MFA indicators. The following two issues were observed: (1) In the accounting of EW-MFA indicators, research work has fully matured at the national level because there is a standardized accounting framework and database, while research work is far from mature at the regional level, including the provincial level and city level, because no unified accounting framework exists. In addition, previous research has mainly focused on direct flow indicators, such as direct material input and domestic material consumption, while not sufficiently focusing on comprehensive indicators, which aggregate direct flow indicators with indirect flow indicators and hidden flow indicators, such as the raw material consumption (RMC) and total material requirement. (2) Fewer studies have examined the driving force and dynamics of EW-MFA indicators than those that have examined the accounting of EW-MFA indicators, and the research methods can be divided into decomposition analysis and regression analysis. For the decomposition analysis of EW-MFA indicators, the IPAT equation, index decomposition analysis (IDA), and structure decomposition analysis (SDA) are employed. The IPAT equation is the most commonly used method for analyzing the driving force of EW-MFA indicators; however, this equation can hardly reveal the effect of economic structure and technology in the economic system on EW-MFA indicators. IDA and SDA can overcome this deficiency; however, thus far, there have been few such studies. For the regression analysis of EW-MFA indicators, no consistent conclusions concerning which factors are the driving forces of EW-MFA indicators have been drawn, although some factors have been frequently suggested as affecting resource productivity, such as income level and population density. Finally, we propose the directions for future research by summarizing the shortcomings of the current research on EW-MFA with respect to the following goals: (1) disaggregating EW-MFA data to economic sectors; (2) promoting research on accounting for comprehensive indicators of EW-MFA, especially for RMC; (3) developing an accounting framework of EW-MFA on the regional level; and (4) stimulating research on the driving forces and dynamics of EW-MFA indicators.