Extracellular polymeric substances (EPS) are one of the main components of biofilm, prompting biofilm to form a cohesive three-dimensional framework. Numerous methods are available to help characterize the properties and the structural, chemical and physical organizations of EPS during the biofilm formation process. This review highlights key techniques from different disciplines that have been successfully applied in-situ and non-destructively to describe the complex composition and distribution of EPS in biofilm, especially microscopic, spectroscopic, and the combination of multi-disciplinary methods that can provide new insights into the complex structure/function correlations in biofilms. Among them, confocal laser scanning microscopy (CLSM) is emphasized, and its principles, applications, advantages, and limitations are summarized. Multidisciplinary techniques have been developed and recommended to study EPS during the biofilm formation process, providing more in-depth insights into the composition and spatial distributions of EPS, so as to improve our understanding of the role EPS plays in biofilms ultimately.