This study explores the gelation mechanisms of high and low acyl gellan gum (HAGG and LAGG) by analyzing their chain conformations and self-assembly behaviour during cooling. Using statistical analysis of atomic force microscopy (AFM) images, differential scanning calorimetry (DSC), and rheological measurements, we examined the cooling process from 90 °C to 25 °C for HAGG and from 90 °C to 10 °C for LAGG. Both types of gellan gum transitioned from single-stranded chains to double-helical structures. HAGG exhibited semi-flexible single and double-helical chains with shorter persistence lengths, prominent kinks, and larger kink angles, forming double helices through intra- and interchain interactions. These helices then underwent side-by-side self-assembly into multi-branched, elastic networks. Conversely, LAGG displayed more rigid chains with longer persistence lengths, fewer kinks, and smaller kink angles, forming double helices via interchain interactions, followed by side-by-side self-assembly into less-branched, rigid networks. AFM directly visualized these structural transitions, notably the side-by-side self-assembly for the first time, supported by DSC and rheological data. The results provide new evidence on gellan gum's gelation mechanisms and self-assembly behaviour in pure water.