Literatures of preview works at city-level, or urban material flow analysis (MFA) are reviewed since 1965, when Wolman first used the word “metabolize” to describe the socioeconomic system. Although there are a lot of studies on urban MFA and a remarkable achievement was made, only very few works focused on the framework of urban MFA. It is the key issue about current studies on urban MFA that lacking a suitable framework which is based on the characters of a city and focus on the core problem on the sustainability of urban area. Especially for China, almost all of the works on urban MFA were based on the national-level MFA framework which is not appropriate for city-level MFA, because the characters of a city are very different from those of a country. Base on the work of reviewing the existed MFA framework, a new framework is set for urban MFA. The objective of this framework is to focus on the sustainability of urban socio-economic systems, as well as their interaction with the regional-level sustainable development. Different from other MFA frameworks which just quantify total material flows into and out of a city, this framework characterizes the inherent specificities of the material flows on a city level. Recycling and recyclable waste flows and water flows are important elements in this framework, attempting to quantify the input and output flows of recycling and recyclable waste as well as water of a city. It also tries to quantify the internal recycling flows of the city studied. However, the dependences on local and foreign resources, wastes, as well as emissions to air and water of the city investigated are key elements for this framework. This study identifies key issues related to the system boundary and the measurement of specific mass flows between the national-level MFA and the urban-level MFA. The system boundary of an urban-level MFA research is composed by physical boundary and logical boundary which mainly refers to the human economical activity, e.g. agriculture activity, industrial production, human life, etc. For details, methods on determining attribute for special mass flows, such as direct energy input and output flows, flows caused by transportation and logistics industry, and flows based on the share of infrastructures are proposed. A new indicator system is established, with increased attention to the city′s sustainability. Although it is based on the indicator system for national-level MFA, the most important improvement of this indicator system is that some new indicators are added, such as secondary resource inputs, internally recycled resources, fresh water consumption, recyclable waste output, reused waste water, and local resource output, in order to measure the sustainable development ability of urban area. The change in values of indicators can represent the variations in the sustainability of the city studied.