A series of polyether based siloxane surfactants with different branched chain and alkyl groups were synthesized by thiol-ene reaction and Piers-Rubinsztajn reaction. The effect of the siloxane structures (alkyl groups and branched chains) on the adsorption and aggregation behavior in aqueous solution was investigated by surface tension, fluorescence, dynamic light scattering (DLS), freeze-fracture transmission electron microscopy (TEM), and TEM. The molecular structures of siloxane can obviously influence their surface activities and thermodynamics. Replacing the methyl of trimethylsiloxyl groups with longer alkyl groups (ethyl, propyl, and butyl) and branching trimethylsiloxyl resulted in an obvious decrease of the values of critical micelle concentration (CMC) and surface tension at CMC (gamma(CMC)). Dense surface films packed with CH3 groups result in the lower surface tensions being disordered by longer alkyl groups or branched chains of siloxane hydrophobic groups. And the minimum surface area per surfactant molecule (Amin) values of Si-3-PG, Et-Si-3-PG, Pro-Si-3-PG, and But-Si-3-PG successively decrease about 3.5 A with each increasing - CH2 - group. All polyether based siloxane surfactants can form nonuniform size spheroidal aggregates in aqueous solution. Concerning the driving force, the micellization process was spontaneous but less spontaneous compared with adsorption.