Nanocomposites composed of the cationic polypeptide ε-poly-l-lysine (ε-PL) and natural sodium montmorillonite (MMT) were prepared and evaluated. These MMT/ε-PL composites formed highly ordered nanostructures resembling natural nacreous layers by a simple process. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) analyses confirmed that a small amount of ε-PL remarkably enhanced the MMT orientation in the composites. This MMT orientation-enhancing effect of ε-PL was more pronounced than that of poly(vinyl alcohol) (PVA), which is one of the most popular ingredients of MMT-based composites. The orientation enhancement provided by ε-PL was primarily driven by ionic interactions and responsible for high mechanical properties at low polymer content. This remarkable reinforcing effect of ε-PL on MMT at a low polymer content will help to develop high-performance and sustainable nacreous composites. In addition, it improves our understanding of the reinforcing mechanism of natural nacre, which exhibits excellent mechanical properties even with relatively small amounts of organic component.