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We investigate the direct CP violation for the decay process of B-s→P(V)π0 (P,V refer to the pseudoscalar meson and vector meson, resp.) via isospin symmetry breaking effects from the π0-η-η′ mixing mechanism in PQCD factorization approach. Isospin symmetry breaking arises from the electroweak interaction and the u-d quark mass difference by the strong interaction, which are known to be tiny. However, we find that isospin symmetry breaking at the leading order shifts the CP violation due to the new strong phases.