In this work, the dynamic changes in the composition of fouling layer as a function of operating time were systematically investigated and compared in forward osmosis (FO) based membrane processes for municipal wastewater treatment. Fouled membranes were collected from four different operational cycles (3, 8, 16 and 30 days) and prepared for quantitative analyses of organic and inorganic foulants and microscopic observation by confocal laser scanning microscopy (CLSM). Moreover, the dynamic changes of bacterial concentration and community structure were characterized by the plate count method and Illumina MiSeq sequencing, respectively. The results showed that with the extension of operation time, the amount of organic foulants, inorganic species and bacteria deposited on the membrane surface exhibited a gradual increase trend in direct FO, resulting in a corresponding increase of fouling resistance and decline of water flux. As for OMBR, apart from the organic foulants such as polysaccharides and proteins, both the inorganic species and membrane surface bacterial concentration reached to a plateau phase after 8 days of operation, leading to a much lower fouling resistance and flux reduction. The bacterial community analysis indicated that two dominant genus were detected in the biofilm of OMBR; however, the bacterial community on the membrane surface of direct FO exhibited a significantly higher diversity but with a lower abundance.