We present new anisotropic black brane solutions in 5D Einstein-dilaton-two-Maxwell system. The anisotropic background is specified by an arbitrary dynamical exponent ν, a nontrivial warp factor, a non-zero dilaton field, a non-zero time component of the first Maxwell field and a non-zero longitudinal magnetic component of the second Maxwell field. The blackening function supports the Van der Waals-like phase transition between small and large black holes for a suitable first Maxwell field charge. The isotropic case corresponding to ν = 1 and zero magnetic field reproduces previously known solutions. We investigate the anisotropy influence on the thermodynamic properties of our background, in particular, on the small/large black holes phase transition diagram. We discuss applications of the model to the bottom-up holographic QCD. The RG flow interpolates between the UV section with two suppressed transversal coordinates and the IR section with the suppressed time and longitudinal coordinates due to anisotropic character of our solution. We study the temporal Wilson loops, extended in longitudinal and transversal directions, by calculating the minimal surfaces of the corresponding probing open string world-sheet in anisotropic backgrounds with various temperatures and chemical potentials. We find that dynamical wall locations depend on the orientation of the quark pairs, that gives a crossover transition line between confinement/deconfinement phases in the dual gauge theory. Instability of the background leads to the appearance of the critical points (μϑ,b, Tϑ,b) depending on the orientation ϑ of quark-antiquark pairs in respect to the heavy ions collision line. © 2018, The Author(s).