We extend the holographic analysis of light-baryon spectrum in [50] to the case involving the heavy flavors. With the construction of the Witten-Sakai-Sugimoto model in the D0-D4 background, we use the mechanism proposed in [59,60,61] by including two light and one heavy flavor branes, to describe the heavy-light baryons as heavy mesons bound to a flavor instanton. The background geometry of this model corresponds to an excited state in the dual field theory with nonzero glue condensate TrF ∧ F = 8π 2 N cκ , or equivalently a θ angle, which is proportional to the number density of the D0-brane charge. At strongly coupled limit, this model shows that the heavy meson is always bound in the form of the zero mode of the flavor instanton in the fundamental representation. We systematically study the quantization for the effective Lagrangian of heavy-light baryons by employing the soliton picture, and derive the mass spectrum of heavy-light baryons in the situation with singleand double-heavy baryon. We find the difference in the mass spectrum becomes smaller if the density of D0-brane charge increases and the constraint of stable states of the heavylight baryons is 1 < b < 3. It indicates that baryon can not stably exist for sufficiently large density of D0 charge which is in agreement with the conclusions in the previous study of this model.