Abstract: We investigate D-instanton effects on the holographic Weyl semimetal in a top-down approach. From the free energy of the D7 brane embedding solutions, we get a phase diagram in terms of the electron mass, instanton number, and temperature in the unit of the weyl parameter. We calculate non-linear conductivities from the regularity condition of the probe D7 brane and investigate anomalous Hall phenomena in the boundary system. From the study of the phase diagram, we suggest the gaped phase induced by the instanton to a topological insulator.