In this paper, we consider the convergence rate with respect to Wasserstein distance in the invariance principle for deterministic non-uniformly hyperbolic systems. Our results apply to uniformly hyperbolic systems and large classes of non-uniformly hyperbolic systems including intermittent maps, Viana maps, unimodal maps and others. Furthermore, as a non-trivial application to the homogenization problem, we investigate the Wasserstein convergence rate of a fast–slow discrete deterministic system to a stochastic differential equation.