A method based on the Zernike coefficients transformation is proposed for the wavefront sensing of a sparse aperture system. We deduce a matrix that allows the Zernike transformation between the sub-apertures’ wavefronts and the global counterparts in a sparse aperture system. With the matrix and the given global aberrations, the aberrations of the sub-apertures can be calculated through the transformation. The simulation results indicate that the increase of filling factor of the sparse aperture system could lead to the increase of orders of the Zernike polynomials, which describe the sub-aperture’s wavefront. The root mean square value of the detected Zernike coefficients of the sub-aperture is determined by its azimuth angle when the filling factor is fixed.