The present research was aimed to explore the biocompatibility of IKVAV self-assembling peptide nanofiber scaffold with olfactory ensheathing cells (OECs) of rats. The OECs were seeded onto the surface of coverslips covered with IKVAV self-assembling peptide nanofiber scaffold hydrogel (2D culture system), and implanted within IKVAV self-assembling peptide nanofiber scaffold hydrogel (3D culture system), respectively. The adhesion, viability of OECs were observed with inverted microscope. Then the characteristics for survival and adhesion of cells by image processing were observed, and statistical analysis on the number of S-100 positive cell, the area of the cell bodies and the perimeter of the cell and MTT method were carried out. It was found that the OECs could survive and migrate in IKVAV self-assembling peptide nanofiber scaffold. The result of the cell MTT exam, of the shape and quantity of cells had no significant difference compared to those of the OECs cultured with poly-L-lysine (PLL). It has been proved that IKVAV self-assembling peptide nanofiber scaffold has good biocompatibility with rat OECs.