The cross section of photonic crystal fiber (PCF) is a two dimensional photonic crystal. The rods formed in PCF are not exact cylinders, the shape of rods will affect the eigenmode formed in two dimensional photonic crystals around a defect. Based on the relations between the defect eigenmodes and the radius of dielectric cylinders, the defect eigenmodes in photonic crystals in which the ellipse rods take the place of cylinders are studied by numerical calculation. The analysis of the relation between the eigenfrequency and the minor axis radius of ellipse rods show that the defect eigenfrequency is controlled by the cross section area of rods and the distribution of electromagnetic field around the defect is also affected by the cross section shape of rods. It provides a better way to modify the distribution of electromagnetic fields in photonic crystal and keeps the eigenfrequency unchanged.