Here, we report a novel, programmable, molecular self‐assembling system to fabricate shape‐specific, three‐dimensional nanoarchitectures. Three types of simple 16‐mer peptides consisting of hydrophobic Leu and hydrophilic Lys, LKL16, KLK16, and LK16, were prepared as building blocks for nanofabrications. A detailed analysis of the conformation and self‐assembling mechanism was performed by using circular dichroism (CD), FTIR spectroscopy, and atomic force microscopy (AFM). A wide variety of self‐assembled nanoarchitectures, such as β‐sheet‐plates, β‐sheet‐fibers, α‐helix‐particles, and α‐helix‐plates, could be fabricated by tuning the peptide sequence, reaction time, and solution pH. The ability to control the self‐assembled nanostructures should provide a simple and/or essential insight into the mechanism of peptide aggregation, including amyloid formation, and it should be useful for the design of novel bio‐related nanomaterials.