Research has so far paid little attention to the impact of the drying method on the structural and compositional analyses of biofilms from moving bed biofilm reactors (MBBRs). To ensure that the biofilm was derived from a steady operation phase of the MBBR, in this study, stable values of the chemical oxygen demand (COD), PO43-, total nitrogen (TN), ammonia–nitrogen (NH4-N), NO3-N and NO2-N concentration, and the biofilm dry weight were obtained after 22 d of operation. Four drying methods (supercritical CO2 drying, vacuum freeze-drying, heat drying, and natural drying) were used to pretreat the biofilms, and the changes in biofilm structures and compositions were investigated in detail. The supercritical CO2 drying and vacuum freeze-drying both maintained the biofilm compositions, while vacuum freeze-drying increased the average pore diameter of the biofilm more than five times that of the biofilm obtained by supercritical CO2 drying. In addition, heat drying and natural drying both damaged the structures and compositions of the biofilms, and heat drying in particular could cause structural collapse, surface charge declines of at least 20%, C and N elemental losses, and biomacromolecule (proteins, polysaccharides, and lipids) losses. The results from this investigation will aid in elucidating the appropriate drying methods for analyzing biofilm structures and compositions.