In this work, a nonconventional protein source of pea protein isolate (PPI) was filled with montmorillonite (MMT) and rectorite (REC) by solution intercalation respectively, and then the reinforced PPI-based nanocomposites were produced by hot press. The structure and interaction in the nanocomposites were investigated by FTIR, XRD, DSC, DMA, and pH and Zeta-potential tests whereas the reinforcing effect was verified by tensile test. Furthermore, the origin of enhancing mechanical performances and the effects of layered silicate structure were explored. Although the MMT with lower negative-charge surface and smaller apparent size of crude particles was easier to be exfoliated completely, the exfoliated REC nanoplatelets with more negative-charge could form stronger electrostatic interaction with positive-charge-rich domains of PPI molecules, and hence produced the highest strength in two series of nanocomposites. In this case, the newly formed hydrogen bonds and electrostatic interaction on the surface of silicate lamellas guaranteed the transferring of the stress to rigid layered silicates. The cooperative effect of newly formed physical interaction between layered silicates and PPI molecules as well as the spatial occupancy of intercalated agglomerates of layered silicates destroyed the original microphase structure of PPI matrix and cleaved the entanglements among PPI molecules. It was not in favor of enhancing the elongation and strength.