In this paper, we prove estimates and quantitative regularity results for the harmonic map flow. First, we consider H^1_loc-maps u defined on a parabolic ball P\subset M\times R and with target manifold N, that have bounded Dirichlet-energy and Struwe-energy. We define a quantitative stratification, which groups together points in the domain into quantitative weakly singular strata S^j_{\eta,r}(u) according to the number of approximate symmetries of u at certain scales, and prove that their tubular neighborhoods have small volume, namely Vol(T_r(\cS^j_{\eta,r}(u))< Cr^{m+2-j-\eps}. In particular, this generalizes the known Hausdorff estimate dim S^j(u)< j for the weakly singular strata of suitable weak solutions of the harmonic map flow. As an application, specializing to Chen-Struwe solutions with target manifolds that do not admit certain harmonic and quasi-harmonic spheres, we obtain refined Minkowski estimates for the singular set. This generalizes a result of Lin-Wang. We also obtain L^p-estimates for the reciprocal of the regularity scale. The results are analogous to our results for mean curvature flow that we recently proved.