We investigate three-dimensional focus shaping generated from double-mode cylindrical vector beams with the Gaussian and Bessel-Gaussian pupil apodization functions by choosing the suitable polarization states of beams. Further, we compare them with that generated from the Laguerre-Gaussian pupil apodization function in the same situation. We find that the focus shaping generated from the Gaussian beam has the smallest zero intensity spot size. However, the situation of the Bessel-Gaussian beam not only possesses stability, which makes it suitable when applied in optical trapping, but also shows the best uniformity, which indicates its excellent performance in super-resolution fluorescence microscopy.