The high-order gas-kinetic scheme (HGKS) features good robustness, high efficiency and satisfactory accuracy,the performance of which can be further improved combined with WENO-AO (WENO with adaptive order) scheme for reconstruction. To reduce computational costs in the reconstruction procedure, this paper proposes to combine HGKS with a hybrid WENO-AO scheme. The hybrid WENO-AO scheme reconstructs target variables using upwind linear approximation directly if all extreme points of the reconstruction polynomials for these variables are outside the large stencil. Otherwise, the WENO-AO scheme is used. Unlike combining the hybrid WENO scheme with traditional Riemann solvers, the troubled cell indicator of the hybrid WENO-AO method is fully utilized in the spatial reconstruction process of HGKS. During normal and tangential reconstruction, the gas-kinetic scheme flux not only needs to reconstruct the conservative variables on the left and right interfaces but also to reconstruct the derivative terms of the conservative variables. By reducing the number of times that the WENO-AO scheme is used, the calculation cost is reduced. The high-order gas-kinetic scheme with the hybrid WENO-AO method retains original robustness and accuracy of the WENO5-AO GKS, while exhibits higher computational efficiency.