Economy and environment are linked by material and energy flow, while the imbalance of the flow is the key cause inducing environmental problems. Through tracing and estimating the material input, output and stock within economic-environmental system, material flow analysis can provide a scientific guide to dematerialization and sustainable development. Substance flow analysis (SFA), and material flow accounting and analysis (MFA) are the main types of material flow analysis. SFA tracks the flows of specific substances (e.g., elements or compounds), often with the intent of identifying environmental problems and seeking for potential solutions, while MFA usually regards economic system as a “black box” and analyzes its material throughput. In this review, a detailed description was made on SFA and MFA, and their similarities and differences in methodology and application were analyzed, with the future research directions of material flow analysis discussed.