The open charm and beauty production cross-sections in the deep inelastic ep scattering (DIS) at HERA from the H1 and ZEUS Collaborations are combined. Reduced cross-sections are obtained in the kinematic range of negative four-momentum transfer squared of a photon 2.5≤ Q2 ≤2000 GeV2 and the Bjorken scaling variable 3×10¬5 ≤ xBj ≤5×10¬2. The different charm- and beauty-tagging methods are used for the heavy-flavor production study in DIS. The combined method accounts for the correlations of systematic uncertainties, as well as statistical uncertainties among the different datasets. Perturbative QCD (pQCD) calculations are compared to the measured combined data. A NLO QCD analysis is performed using these data together with the combined inclusive deep inelastic scattering cross-sections from HERA. The running charm- and beauty-quark masses are determined as mc(mc) = 1,290+0,046−0,041(exp /fit)+0,062−0,014(model)+0,03−0,031(parametrization) GeV and mb(mb) = 4,049+0,104−0,109(exp /fit)+0,090−0,032(model)+0,001−0,031(parametrization) GeV.