We propose a scheme for chirality discrimination via a topological invariant. The physical model is based on a three-level subspace of a molecule. By modulating the components of the control field with proper frequencies, two different two-level effective Hamiltonians are derived for the left-handed and the right-handed molecules. We parameterize the effective Hamiltonians with two angles and demonstrate that a topological quantum phase transition can be induced by tuning the effective Rabi frequency if the molecule is right-handed. This phenomenon provides a method to discriminate the chirality of the molecule by measuring a topological invariant, i.e., the Chern number, of the parametric manifold. Since the Chern number is robust against perturbations to the system, the scheme is insensitive to the systematic errors of the control fields, the deviations of the modulation frequencies, and decoherence of the molecule. Therefore, the scheme may provide useful perspectives to construct a robust discriminator of chiral molecules.