Membrane technology has been one of the most promising techniques to solve the water problem in future. Unfortunately, it suffers from the fouling problem which is ubiquitous in membrane systems. The origin of the bewilderments of the fouling problem lies in the lack of deep understanding. Recent studies have pointed out that the molecular structure of foulant affects its fouling propensity which has been ignored in the past. In this study, the filtration behaviors of alginate blocks derived from the same source were comprehensively explored. Alginate blocks share the same chemical composition but differ from each other in molecular structure. The alginate was first extracted from natural seaweed using calcium precipitation and ion-exchange methods. Extracted alginate was further fractionized into MG-, MM- and GG-blocks and the characteristics of the three blocks were examined by Fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FESEM) observations, and transparent exopolymer particles’ (TEPs) measurements. Results showed that MG-, MM- and GG-blocks had the same functional groups, but they showed different intermolecular interactions. TEP formation from MG-, MM- and GG-blocks revealed that the molecule crosslinking of them decreased in the order of MM-blocks > GG-blocks > MG-blocks. It was further found from microfiltration tests that these alginate blocks had completely different fouling propensities which can be explained by the TEP formation. TEPs would accumulate on membrane surfaces and worked as a pre-filter to avoid serious pore blocking of membrane. That all suggested that the membrane fouling was closely related to the molecular structure of foulant. It is expected that this study can provide useful insights into the fouling propensities of different types of polysaccharides during filtration processes.