Multiscale simulation has been conducted for the formation of a surfactant–protein complex that uses sodium dodecyl sulfate (SDS), a negatively charged surfactant, and aquaporin Z (AqpZ), a membrane protein that facilitates water transport across lipid membranes. A detailed analysis of the molecular driving forces of the self-assembly at different pH values reveals distinctive contributions of electrostatic and hydrophobic interactions to the complex structure and formation kinetics. The electrostatic interactions become more significant at low pH and are responsible for the formation of larger complexes. A comparison of the protein conformation in the SDS complex with that in the lipid bilayer of palmitoyloleoyl phosphatidyl ethanolamine (POPE) shows that the SDS molecules have only marginal effects on AqpZ conformation including the water channel structure. The simulation indicates that AqpZ preserves its secondary structures after being bound with SDS molecules, while the arrangement of the helical structures leads to a coiled-coil to single helix transition as suggested by experiments. AqpZ may lose water permeability either due to the blockage of the water channel by individual SDS molecules or due to the attachment of micelle-like structures at the hydrophilic ends of the water pore. Reconstitution of the AqpZ complex into a POPE bilayer shows that the membrane protein regains its activity after the complete removal of SDS molecules from the protein pores. The molecular insights gained from multiscale simulation will be helpful for future development of AqpZ-embedded membranes.