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In this work, we studied the effects of incubation concentration and time on the self-assembly behaviors of regenerated silk fibroin (RSF). Our results showed the assembly ways of RSF were concentration-dependent and there were four self-assembly ways of RSF: (i) At relatively low concentration (≤0.015%), RSF molecules assembled into protofilaments (random coil), and then the thickness decreased and the secondary conformation changed to antiparallel β-sheet; (ii) at the concentration of 0.015%, RSF molecules assembled into protofilaments (random coil), and then assembled into protofibrils (antiparallel β-sheet). The protofibrils experienced the appearance and disappearance of phase periodic intervals in turn; (iii) at the concentration of 0.03%, RSF molecules assembled into bead-like oligomers (random coil), and then assembled into protofibrils (antiparallel β-sheet), and finally the height and phase periodic intervals of RSF protofibrils disappeared in turn; and (iv) at the relatively high concentration (≥0.15%), RSF molecules assembled into protofilaments (random coil), then aggregated into blurry cuboid-like micelles (random coil), and finally self-arranged to form smooth and clear cuboid-like micelles (antiparallel β-sheet). These results provide useful insights into the process by which the RSF molecules self-assemble into protofilaments, protofibrils and micelles. Furthermore, our work will be beneficial to basic understanding of the nanoscale structure formations in different silk-based biomaterials.