Microscopic examination of the activated sludge and morphological characterization of the flocs provides detailed information about the treatment process. The aim of this study is to investigate the morphological parameters of flocs obtained from a thermophilic jet loop membrane bioreactor (JLMBR) in different sludge retention times (SRTs), considering EPS and SMP concentration, hydrophobicity, zeta potential. The results showed that irregularity decreased with the increasing SRT. The compactness value was calculated to be less than 1 for all SRTs. However, the sludge had a more compact structure when the SRT increased. Zeta potential increased whereas hydrophobicity and floc size reduced, with increasing SRT. Furthermore, 2-D porosity calculated using the hole ratio was higher at greater SRTs. Hence, there was a significant correlation between the results obtained using the imaging technique and operation conditions of thermophilic JLMBR.