We thoroughly analyze the number of independent zero modes and their zero points on the toroidal orbifold () with magnetic flux background, inspired by the Atiyah-Singer index theorem. We first show a complete list for the number of orbifold zero modes belonging to eigenvalue . Since it turns out that quite complicatedly depends on the flux quanta , the Scherk-Schwarz twist phase , and the eigenvalue , it seems hard that can be universally explained in a simple formula. We, however, succeed in finding a single zero-mode counting formula $n_{\eta} = (M-V_{\eta})/N + 1V_{\eta}$ denotes the sum of winding numbers at the fixed points on the orbifold . The formula is shown to hold for any pattern.

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