  The notion of a $F$-manifold algebras is an algebraic description of a
$F$-manifold. In this paper, we introduce the notion of Hom-$F$-manifold
algebras which is generalisation of $F$-manifold algebras and Hom-Poisson
algebras. We develop the representation theory of Hom-$F$-manifold algebras and
generalize the notion of Hom-pre-Poisson algebras by introducing the
Hom-pre-$F$-manifold algebras which give rise to a Hom-$F$-manifold algebra
through the sub-adjacent commutative Hom-associative algebra and the
sub-adjacent Hom-Lie algebra. Using $\huaO$-operators on a Hom-$F$-manifold
algebras we construct a Hom-pre-$F$-manifold algebras on a module. Then, we
study Hom-pre-Lie formal deformations of commutative Hom-associative algebra
and prove that Hom-$F$-manifold algebras are the corresponding semi-classical
limits. Finally, we study Hom-Lie infinitesimal deformations and extension of
Hom-pre-Lie $n$-deformation to Hom-pre-Lie $(n+1)$-deformation of a commutative
Hom-associative algebra via cohomology theory.
