Bound states in the continuum (BICs) are perfectly localized resonances despite embedding in the continuum spectrum. However, an isolated BIC is very sensitive to the structure perturbation. Here, we report merging acoustic BICs in a single open resonator, robust against the structure perturbation. We find that both symmetry-protected BIC and Friedrich-Wintgen BIC are sustained in a single coupled waveguide-resonator system. By varying the height and length of the resonator, these two BICs move toward each other and merge into a single one at a critical dimension. Compared to an individual BIC, the merged BIC is robust against fabrication error because its Q-factor is proportional to ΔL−4, where ΔL embodies the structure perturbation. The essence of this extraordinary phenomenon is perfectly explained by the two- and three-level approximations of the effective non-Hermitian Hamiltonian. Finally, we present direct experimental demonstrations of the moving and merging of BICs in a coupled 3D waveguide-resonator, which are evidenced by the vanishing of the linewidth of Fano resonance in the transmission spectra. Our results may find exciting applications in designing high-quality acoustic sources, sensors and filters.