In　this　paper,　we　consider　the　numerical　approximations　for　a　hydrodynamical　model　of　smectic-A　liquid　crystals.　The　model,　derived　from　the　variational　approach　of　the　modified　Oseen-Frank　energy,　is　a　highly　nonlinear　system　that　couples　the　incompressible　Navier-Stokes　equations　and　a　constitutive　equation　for　the　layer　variable.　We　develop　two　linear,　second　order　time　marching　schemes　based　on　the　Invariant　Energy　Quadratization　method　for　nonlinear　terms　in　the　constitutive　equation,　the　projection　method　for　the　Navier-Stokes　equations,　and　some　subtle　implicit-explicit　treatments　for　the　convective　and　stress　terms.　Moreover,　we　prove　the　well-posedness　of　the　linear　system　and　their　unconditionally　energy　stabilities　rigorously.　Various　numerical　experiments　are　presented　to　demonstrate　the　stability　and　the　accuracy　of　the　numerical　schemes　in　simulating　the　dynamics　under　shear　flow　and　the　magnetic　field.