We study topological objects in holographic QCD based on the Sakai-Sugimoto model, which is constructed with $N_c$ D4 branes and $N_f$ D8/$bar{rm D8}$ branes in the superstring theory, and is infrared equivalent to 1+3 dimensional massless QCD. Using the gauge/gravity duality, holographic QCD is described as 1+4 dimensional U($N_f$) gauge theory in flavor space with a background gravity, and its instanton solutions correspond to baryons. First, using the Witten Ansatz, we reduce holographic QCD into a 1+2 dimensional Abelian Higgs theory in a curved space and consider its topological aspect. We numerically obtain the Abrikosov vortex solution and investigate single baryon properties. Second, we study a single meron and two merons in holographic QCD. The single meron carrying a half-integer baryon number is found to have a infinite energy also in holographic QCD. We propose a new-type baryon excitation of the two-merons oscillation in the extra-direction of holographic QCD.