The effects of oxide aperture shape whose size is small, on the mode characteristics of external cavity oxide-confined photonic crystal vertical cavity surface emitting laser (VCSEL) is studied extensively based on the finite-difference time-domain algorithm. A new three-dimensional model of optical field in photonic crystal VCSEL is built and the influence of the variation in aperture shape on the characteristics of far-field and spectrum is pointed out. It is found that the modal characteristics of PhC-VCSEL are influenced by the shape of oxide aperture, the influence on spectrum feature is more apparent. It can be explained from the distribution of modal field by the fact that the symmetrical characteristic of prismatic oxide aperture is not identical to that of high-order mode. But the influence is less apparent while the depth of photonic crystal hole is deeper. The reason for this matter is illustrated. The results can be used to guide the fabrication of external cavity oxide-confined photonic crystal VCSELs.