The model of full vector Galerkin finite element method (FEM) with transparent boundary conditions (TBC) is established. The modal birefringence, confinement loss and dispersion of the fundamental mode of five kinds highly birefringent photonic crystal fibers (PCFs) with elliptical cores are analyzed and compared. The modal birefringence of a photonic crystal fiber, which is formed by diminishing air holes along x-direction and enlarging air holes along y-direction in inner cladding, is 5.96×10-3 at the wavelength of 1550 nm, while that of a photonic crystal fiber with elliptical core is 1.52×10-3. The results show that high birefringence can be obtained by increasing the difference of air holes size along orthogonal direction in inner cladding. It is also proved that enlarged air holes of inner cladding reduce the confinement loss, and increase the dispersion, but the impact of diminished air holes is reversed; the fewer the air holes in inner cladding are, the flatter the dispersion is.