We thoroughly analyze the number of independent zero modes and their zero points on the toroidal orbifold $T^2/mathbb{Z}_N$ ($N = 2, 3, 4, 6$) with magnetic flux background, inspired by the Atiyah-Singer index theorem. We first show a complete list for the number $n_{eta}$ of orbifold zero modes belonging to $mathbb{Z}_{N}$ eigenvalue $eta$. Since it turns out that $n_{eta}$ quite complicatedly depends on the flux quanta $M$, the Scherk-Schwarz twist phase $(alpha_1, alpha_2)$, and the $mathbb{Z}_{N}$ eigenvalue $eta$, it seems hard that $n_{eta}$ can be universally explained in a simple formula. We, however, succeed in finding a single zero-mode counting formula $n_{eta} = (M-V_{eta})/N + 1$, where $V_{eta}$ denotes the sum of winding numbers at the fixed points on the orbifold $T^2/mathbb{Z}_N$. The formula is shown to hold for any pattern.
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