The　effect　of　the　material　lattice　structure　during　the　laser　nano-structuring　is　generally　overlooked.　Here,　we　reveal　the　energy　band　structure　perturbation　at　different　polarizations,　and　its　underlying　mechanism　functioning　on　the　ultrafast　laser　nano-structuring.　This　phenomenon　is　confirmed　by　the　variation　in　deviation　of　femtosecond　laser-induced　periodic　surface　structures　(LIPSS)　orientation　on　thin-film　lithium　niobate　(LiNbO3).　An　increase　in　the　laser　fluence　leads　to　a　notable　enlarging　in　the　effective　bandgap　of　LiNbO3　from　3.78　to　5.70　eV,　weakening　the　impact　of　polarization-dependent　intrinsic　perturbations　within　LiNbO3　that　contribute　to　the　deviation　of　LIPSS　orientation.　Precise　writing　of　polarization　dependent　structures　and　selective　reading　of　corresponding　information　are　realized　via　directional　modulation　of　LIPSS.　The　study　of　energy　band　structure　perturbation　effect　develops　a　novel　mechanism　for　the　deviation　angle　modulation　of　nano-structuring　at　the　accuracy　compensation　within　1　degrees,　thus　promising　enhanced　precision　for　future　laser　nano-structuring　applied　in　advanced　nano-optics　devices.