We use Hypergeometric Gaussian-II (HyGG-II) modes to investigate the impacts of non-Kolmogorov atmospheric turbulence on the Holevo channel capacity of a quantum communication scheme. The capacity of HyGG-II modes can be higher than that of Laguerre–Gaussian modes via modulating the hollowness parameter. The influences of low-order turbulence aberrations including tilt, defocus, astigmatism, and coma on the capacity are also explored. Generally, tilt aberration dominates among all low-order aberrations and defocus and astigmatism aberrations are always negligible. By contrast, the effect of coma aberration can be enhanced to be non-negligible when the turbulence strength or the channel zenith angle is enhanced. We also show that only the total and tilt aberrations are sensitive to the non-Kolmogorov power-law exponent. Our results may contribute to the quantum optical communication as well as aberration compensation in turbulent channels utilizing the novel family of vortex beams.